Washington has said that it is "deeply concerned" after Bahrain ordered a top US diplomat to leave the country after he met with a leading Shia opposition group, Al Jazeera reported.
Bahrain's foreign ministry said in a statement on Monday that US Assistant Secretary of State for Democracy, Human Rights and Labour Tom Malinowski is not welcome in the country.
It said he had intervened in the country's domestic affairs by holding meetings with some groups at the expense of others.
Malinowski, who arrived in the country on Sunday and had been scheduled to stay for three days, was ordered to leave after meeting with Bahrain's Shia opposition group, Al-Wefaq.
In a statement on Monday, US State Department spokeswoman Jen Psaki said: "The United States is deeply concerned by ... Bahrain's decision to demand the immediate departure of Tom Malinowski.
"Assistant Secretary Malinowski's visit to Bahrain had been coordinated far in advance and warmly welcomed and encouraged by the government of Bahrain.
"Contrary to our longstanding bilateral relationship and in violation of international diplomatic protocol, the government insisted - without advance warning and after his visit had already commenced - to have a Foreign Ministry representative present at all of ... Malinowski's private meetings with individuals and groups representing a broad spectrum of Bahraini society.
"These actions are not consistent with the strong partnership between the United States and Bahrain."
Bahrain, a tiny island nation that is home to the US Navy's 5th Fleet, has been roiled by near-daily protests by Shias seeking greater political rights and inspired by the Arab Spring wave of revolutions since early 2011.
The government moved to crush the uprising, which threatened to spill into neighbouring Saudi Arabia and other Gulf countries with Shia populations, with the help of regional Gulf Arab forces.
Repeated rounds of political talks have failed to significantly close the rifts between the country's Sunni monarchy and majority Shia factions.
Bahrain's foreign ministry said the kingdom's relations with the US remain strong and important but such meetings were divisive.
Malinowski's actions, added the statement, "run counter to conventional diplomatic norms".
Al-Wefaq spokesman Abdul Jalil Khalil told the AP news agency that Malinowski met with the group on Sunday evening and was scheduled to hold a joint meeting with them and other opposition groups on Tuesday.