The president of Mexico sent a formal complaint to the United States for "interventionism" shortly before he met with Kamala Harris to discuss immigration.
President Andres Manuel Lopez Obrador said at a press conference on Friday morning that the US was "promoting coup plotters" by funding an anti-corruption group undermining his government.
“It is an interventionist act that violated our sovereignty,” said Mr López Obrador, who announced that Mexico had filed a diplomatic note with the US Embassy.
"That’s why we’re asking that (the US government) clarifies this for us. A foreign government can’t provide money to political groups," he added, according to Reuters.
He held up tax records he claimed showed payments from the US Agency for International Development (USAID) to Mexicans Against Corruption and Impunity (MCCI).
Soon after he was speaking to Ms Harris about the surge of migrants on their shared border.
"Together, we must fight violence we must fight corruption and impunity," Ms Harris said during the meeting.
Asked at his earlier press conference if he thought the US government was seeking to remove him from office, Mr López Obrador said he didn’t believe so. He said he wouldn’t raise the issue during the meeting with Ms Harris, which focused on immigration.
The one-page diplomatic note, reviewed by Reuters, said Mexico supported the "essential" work of civil society organizations against corruption, but that MCCI was a political actor.
The note called on the US to confirm financial support through USAID and, if so, to suspend it. Mr López Obrador said people connected to the group “have been explicit in their political militancy against the government of Mexico".
The organization has been critical of the president’s initiative to cancel a partially built airport in Mexico City while constructing a tourist train around the Yucatan Peninsula.
Additional reporting by Associated Press.