Tom Malinowski, US Assistant Secretary of State for Democracy, Human Rights and Labor, said the decision was " about undermining dialogue " in the country.
The diplomat met members of al - Wefaq, which the foreign ministry said was an intervention in domestic affairs.
Protests by members of the majority Shia population have been ongoing.
" Seems #Bahrain government decision not about me but about undermining dialogue, " Malinowski tweeted on Tuesday.
" Those committed to reconciliation should not be deterred, " he added.
Malinowski arrived in Bahrain on Sunday for a three - day trip and was expected to leave later on Tuesday, according to US officials.
While there, the diplomat had meetings scheduled with al - Wefaq, government officials, and a leading human rights activist, Nabeel Rjab.
In meeting al - Wefaq, Malinowski ' s actions ran " counter to conventional diplomatic norms ", the foreign ministry argued.
On Monday, US state department spokeswoman Jen Psaki said the US was " deeply concerned " by Bahrain ' s demand.
The government of Bahrain " is well aware that US government officials routinely meet with all officially recognized political societies, " she said.
The small island nation - located near the Arabian Peninsula - has experienced frequent protests by Shias who seek enhanced political rights.
Political talks have thus far failed to mend rifts between the Shia factions and the monarchy.
Despite the diplomatic clash, Bahrain ' s foreign ministry provided assurances relations with the US remain sound.
" The government of Bahrain asserts that this should not in any way affect the two countries ' relationship of mutual interests, " according to a statement on Monday.
Bahrain, an American ally in a volatile region, is currently home to the US Navy ' s Fifth Fleet.