CAIRO — The U.S.-Egyptian relationship has been through some rocky months since the June 30 military coup that toppled President Mohamed Morsi and the Muslim Brotherhood. But the strain doesn’t seem to have diminished cooperation between the two countries’ intelligence services.

Gen. Mohammed Farid el-Tohamy, the director of Egypt’s General Intelligence Service, said had been “no change” in his organization’s relationship with U.S. spy agencies, despite delay of some U.S. weapons deliveries to the Egyptian military and talk of new Egyptian military contacts with Russia.

“Cooperation between friendly services is in a completely different channel than the political channel,” Tohamy said. “I’m in constant contact with [Director] John Brennan at the CIA and the local station chief, more than with any other service worldwide.”

This fraternal U.S.-Egyptian intelligence relationship is a throwback to the bonds that existed under President Hosni Mubarak. At that time, the charismatic Omar Suleiman was intelligence chief here, and there was a mutual focus on counter-terrorism issues that arguably contributed to Mubarak’s isolation from his people—and to the United States being blindsided by the uprising that topped him in February 2011.

Tohamy is a gaunt, balding man with deep-set eyes and the intense, reserved manner shaped by a lifetime in the shadows. Thin-faced, wearing rimless glasses and chain-smoking through much of the interview, he spoke through a translator in a low bass voice. Tohamy used what he said was his first press interview ever to make some basic points about how intelligence is working in Egypt under Gen. Abdel Fatah al-Sissi, the defense minister who toppled Morsi in June. Tohamy is said to have been one of Sissi’s mentors when the two served in military intelligence; one of Sissi’s first moves after the coup was to bring Tohamy out of retirement into the intelligence post, replacing Morsi’s nominee. This “back to the future” aspect of the new Egypt was also clear in Tohamy’s comment that the Interior Ministry’s domestic security force had “restored some of its former professional capability” by rehiring former officials who had been sacked by Morsi.

Under Mubarak, Tohamy had the delicate job of running the Administrative Oversight Authority, an anti-corruption body, which gave him access to the regime’s most sensitive secrets. Critics have argued that in that role, he helped bury financial improprieties involving Mubarak’s inner circle, a charge Tohamy’s supporters have denied.

I asked Tohamy about the danger that the bloody crackdown on the Muslim Brotherhood will drive its members underground into new versions of the terror organizations that spawned al-Qaeda a generation ago. He answered that some cells loosely affiliated with al-Qaeda were, in fact, trying to take root now in the Sinai Peninsula. Tohamy cited a group called the “Beit el-Maqdis Battalion,” as one of the organizations that claims affiliation with al-Qaeda. But he said there was no evidence the group had “direct communication” with core al-Qaeda or its Egyptian-born leader, Ayman Zawahiri. Instead, communication is through Internet sites and social media. Today, “al-Qaeda represents ideology more than organization,” he said.

Despite the loose structure of these would-be al-Qaeda affiliates, Tohamy continued, “eradicating their cells in Sinai could take some time.” He said the army, which conducts the Sinai operations, had recently had “good results,” but he wouldn’t offer details. He added that some of the jihadist cells had infiltrated Cairo, the Nile Delta and upper Egypt — but said they were being tracked the Interior Ministry.

Tohamy said that terrorist attacks will likely target Egypt’s main sources of foreign income: tourism, the Suez Canal and foreign investment. For that reason, he said, the military and security services must provide special protection for these sectors.

I asked Tohamy whether he would allow Muslim Brotherhood supporters to participate in politics through their “Freedom and Justice Party,” so that they have an alternative to violence. He answered that under Egypt’s “roadmap” for restoring civilian democracy, “no power will be excluded from the political process.” When I pressed about the Freedom and Justice Party, he responded: “Whoever wants to engage in the political process, he is most welcome.”

Whether Egypt is really willing to allow a political voice for the Islamists will be one of the key tests for the new government. So it was notable that the intelligence chief, perhaps the toughest face of the new regime, was willing to support the idea.

Looking outside of Egypt’s borders, Tohamy expressed deep concern about instability in two of the country’s Arab neighbors, Libya and Syria. He said there was a “major security vacuum in Libya,” with tribal militias and radical groups holding power. The collapse of central authority there was “similar to Iraq, exactly,” and stability won’t return unless outside powers help “rebuild the Libyan army and central government.” He warned that “the biggest danger is division of the country,” with Libya splitting in two or more pieces.

As for Syria, Tohamy said efforts to assist the moderate opposition with weapons and money have backfired by instead strengthening the al-Nusra Front, an al-Qaeda affiliate. “Because al-Nusra was more powerful, they captured the weapons.” He argued that the only solution in Syria was a negotiated settlement that would create a new government strong and broad-based enough to go after the al-Qaeda fighters.

“The longer it takes to confront this issue [in Syria], the longer the aftershocks,” he warned.