Tom Malinowski, the assistant secretary of state for the Bureau of Democracy, Human Rights, and Labor. (State Department via AP)

The Bahraini government declared a visiting senior U.S. diplomat persona non grata Monday after he met with representatives of a Shiite opposition party, and it took the highly unusual step of demanding his immediate departure from the tiny Persian Gulf kingdom.

Bahrain’s Foreign Ministry said in a statement that Tom Malinowski, the assistant secretary of state for the Bureau of Democracy, Human Rights, and Labor, had “intervened flagrantly in Bahrain’s internal affairs” by meeting with a political party “to the detriment of other interlocutors.”

The State Department said Malinowski remained in Bahrain on Monday evening while U.S. diplomats in the capital, Manama, sought clarification from Bahraini officials about the request. Governments sometimes declare senior diplomats persona non grata after serious policy disputes. But American officials appeared blindsided by such a public rebuke from a nominal ally that hosts the U.S. 5th Fleet and has acquired $1.4 billion worth of U.S. military equipment since 2000.

Malinowski, who joined the State Department in April, had been the head of Human Rights Watch in Washington for more than a decade. In his former job, he was critical of Bahrain’s violent suppression of a years-long quest by Shiites, a majority in the Sunni-run kingdom, for more political power.

Foreign Policy published an article under Malinowski’s byline in May 2012 describing the tumult he and his colleagues witnessed on a visit to the country, where an opposition movement that flared up during the early days of the Arab Spring in 2011 continues to demand greater political freedoms.

“As we would see during our visit, police torture and abuse have simply moved from police stations to the alleyways and back lots of Shiite villages,” Malinowski wrote in the piece, titled “Prison Island.” “The courts have agreed to retry key opposition leaders, but the government still refuses to release them, though their convictions were based on nothing more than the content of their speeches and participation in meetings and rallies challenging the monarchy.”

The current trip, which began Sunday, is Malinowski’s first to the country in his new job. State Department spokeswoman Jen Psaki said Monday that Malinowski had traveled to Bahrain to express support for reform and reconciliation initiatives that King Hamad bin Isa al-Khalifa’s government has vowed to undertake.

Psaki said in a statement Monday night that the United States was “deeply concerned” by Bahrain’s move. She said the Bahraini authorities demanded that a Foreign Ministry official accompany Malinowski to all his meetings, a request she described as “contrary to our longstanding bilateral relationship and in violation of international diplomatic protocol.”

The State Department wouldn’t say Monday night whether it would acquiesce to the demand.

Malinowski has made no public remarks during the trip. He met with representatives of al-Wefaq, a Shiite political movement that has played a leading role in demonstrations against the monarchy. He planned to meet with government officials and other political figures during the remainder of his trip, which was scheduled to last three days.

The Bahraini government’s statement accused Malinowski of “contravening diplomatic norms and flouting normal interstate relations.”

It ended on a somewhat conciliatory note, saying that it valued the “solid and firm relations bonding the Kingdom of Bahrain and the United States of America” and “stressing the necessity of averting all that mars steadily-growing relations in all fields.”

The United States has criticized Bahrain’s crackdown on Shiite demonstrators, but senior U.S. officials have made clear how much they value a defense partnership that allows them to keep a robust military footprint near Iran.