The swift unraveling of a U.S.-Chinese deal over blind activist Chen Guangcheng has highlighted a persistent problem in the United States’ dealings with China: Diplomats who speak for Beijing have no sway over a Chinese security apparatus beholden only to the upper reaches of the ruling Communist Party.

Assurances that Chen would be treated humanely after his departure Wednesday from the U.S. Embassy in Beijing were “clearly lacking political authority,” said Nicholas Bequelin, senior Asia researcher for Human Rights Watch. “This is a party matter, not a government matter. . . . Only the highest levels of the party can offer guarantees to make an exception for Chen Guangcheng to what is a policy of systematic repression of dissidents in China.”

Instead, Assistant Secretary of State Kurt Campbell and other U.S. diplomats negotiated Chen’s fate with Cui Tiankai, a vice minister at the Foreign Ministry, one of the weakest departments in the Chinese government and one that has been repeatedly big-footed and, on occasion, humiliated by China’s powerful and lavishly funded security apparatus.

China’s foreign minister, Yang Jiechi, sits on neither the Politburo nor its nine-member Standing Committee, the supreme decision-making body. The party makes all key decisions, dictating policy through a cluster of secrecy-shrouded committees and “working groups” that stand above government departments nominally responsible for setting policy. Foreign officials have little direct contact with Communist Party structures and conduct business through weak Chinese government agencies.

Jeffrey A. Bader, a senior fellow at the Brookings Institution who served as director for East Asian affairs on President Obama’s National Security Council until April last year, said the United States has no choice but to work with China’s Foreign Ministry on questions relating to dissidents.

“The ministry is the designated channel of interaction with the U.S. government on these kinds of issues,” he said. “They were in 1989 when we dealt with [dissident astrophysicist] Fang Lizhi and also every dissident since. But they don’t act as a free agent. They go back and coordinate in whatever fashion they do.”

The Foreign Ministry, Bader noted, negotiated and delivered a deal that allowed Fang to leave China after more than a year holed up in the U.S. Embassy in Beijing. “The question is always whether the Foreign Ministry can deliver,” Bader said. “They cannot deliver without a coordinated position.”

Chen, who is in a hospital in Beijing, and other dissidents fall within the orbit of China’s Public Security Bureau and Ministry of State Security, which are supervised by the Communist Party’s Political and Legislative Affairs Committee. The head of that committee, Zhou Yongkang, sits on the Politburo Standing Committee.

When security agents roughed up foreign journalists early last year in central Beijing after anonymous calls on the Internet for a “jasmine revolution,” Yang, the foreign minister, categorically denied any such incidents, despite video footage and other evidence to the contrary.

The disconnect was again on display in February when Cui, the vice foreign minister who negotiated this week over Chen, commented on the flight to the U.S. Consulate in Chengdu of former Chongqing police chief Wang Lijun. Cui insisted that the affair was an “isolated incident” of no significance and had been “resolved, and resolved quite smoothly.”

Nearly three months later, however, aftershocks of the saga continue to shake the leadership. Wang has not been seen in public since he was hustled to Beijing by Ministry of State Security officials soon after he left the Chengdu consulate. Bo Xilai, Wang’s former boss in Chongqing, has been purged from the Politburo and Central Committee in what has become the party’s most serious bout of political turbulence since the Tiananmen Square protests in 1989. Bo’s wife, meanwhile, has been arrested on suspicion of murder.

Chinese diplomats “have no authority” in matters relating to dissidents, and it “is incredible that the U.S. would take their assurances [over Chen] seriously,” said Bequelin of Human Rights Watch. Negotiating over Chen’s future status in China “with a vice foreign minister should have rung loud alarm bells for the U.S.,” as any guarantees relating to the legal activist and his family “would be respected only if they were backed by instructions from the very top of the party,” he said.

Immediately after his escape from de facto house arrest in his home village in Shandong province, Chen acknowledged this reality by making a personal appeal to Premier Wen Jiabao, a member of the Politburo Standing Committee. In a video message released after he took shelter with U.S. diplomats in Beijing, Chen begged Wen to investigate Shandong officials who he said had repeatedly beaten him and his wife, and he asked the premier to guarantee the safety of his family. On Tuesday, according to U.S. Ambassador Gary Locke, Chen rejected an initial deal proposed by the Foreign Ministry and said he needed to speak first to Wen directly. Chen later dropped this demand.

China has not spelled out publicly what private assurances it gave to encourage Chen to leave the U.S. Embassy. A senior State Department official, speaking in Beijing on Wednesday on the condition of anonymity, said China had “acknowledged that Mr. Chen will be treated humanely while he remains in China” and would be allowed visits by American doctors and embassy staff members during his time in the hospital. Locke added Thursday that the deal also included a provision that “the Chinese government would listen to his complaints of abuse and conduct a full investigation.”

But neither Wen nor any other senior party official has said a word in public about Chen’s case since he fled last week. Chen sheltered in the U.S. mission for six days and is receiving treatment in Beijing’s Chaoyang hospital for injuries he suffered during his escape. As soon as he left the embassy, he came under pressure from Chinese security forces, with plainclothes agents reportedly barging into his hospital room. U.S. diplomats were initially allowed to visit Chen at the hospital but have since been barred from the premises, though they have been able to communicate with him by telephone.

In an interview from the hospital with Britain’s Channel 4 News, Chen complained that “nobody from the [U.S.] Embassy is here. I don’t understand why. They promised to be here.” He also said that security agents had infested the family home in Shandong, turning “our home into a prison” equipped with seven surveillance cameras and an electric fence. He later told CNN that, after arriving at the hospital, he learned that following his escape, police officers tied his wife, Yuan Weijing, to a chair for two days and threatened to beat her to death with clubs. His wife has since been allowed to travel to Beijing to join Chen.

The limited clout of China’s Foreign Ministry has been a recurring theme in bilateral relations since the early 1970s, when Henry Kissinger set about reversing decades of hostility. This weakness has sometimes worked to the United States’ advantage. In his book “On China,” Kissinger recalled how China’s diplomats initially opposed allowing Chinese table tennis players to reach out to their American counterparts during a 1971 tournament in Japan. Mao Zedong, roused from a deep slumber induced by sleeping pills, countermanded his own diplomats’ line, telling his nurse to telephone the Foreign Ministry and order it to “invite the American [ping-pong] team to visit China.”

On issues involving human rights, however, the Foreign Ministry’s inability to accurately convey official thinking has caused frustration in Washington. An April 2006 diplomatic cable released by the anti-secrecy Web site WikiLeaks described how the U.S. charge d’affaires, David S. Sedney, the embassy’s No. 2 officer in Beijing, had “raised reports of Chen’s detention” with the Foreign Ministry and been assuredby the ministry’s director general for North American affairs, Liu Jieyi, that the activist “was not in detention.” At the time, Chen had, in fact, been placed under house arrest, a condition that continued until his formal arrest in June 2006.

Sedney, according to the leaked cable, noted reports that contradicted the ministry’s assurance and “emphasized that not being able to trust clear statements by MFA [Ministry of Foreign Affairs] officials damages our ability to work with China.” Assistant Foreign Minister He Yafei, according to the cable, “expressed surprise” and said he, too, thought that Chen had been released and “promised to look into the matter.”

Chen was finally freed from formal detention more than three years later, after being convicted on trumped-up charges of disturbing traffic. His release from prison in 2010 was followed by extralegal detention, a lengthy ordeal of harsh house arrest that featured frequent beatings and that ended only with his flight to Beijing last week. Friends, supporters and journalists who tried to visit before his escape were driven away, often with violence, by plainclothes security officers and hired local thugs.

Throughout, the Foreign Ministry denied anything was amiss, at least in its public statements. It commented on Chen’s flight to the U.S. Embassy only after he had left.

The United States, said ministry spokesman Liu Weimin on Wednesday, should “apologize, carry out a thorough investigation into the incident, deal with those responsible and promise not to let similar incidents happen again.” Liu had no comment Thursday on reports that Chen, who initially refused to consider going abroad, had changed his mind and now wants to leave for the United States.

“I have no information about that,” the spokesman said.