Milorad Dodik said the U.S. Agency for International Development (USAID) was implementing its aid program through non-government organizations to conceal what he said was its real agenda of countering Russian influence in the region.
"Aiming to directly interfere in internal affairs of the Republika Srpska and Bosnia, USAID ... tries to avoid all institutions and to grant funds under cover of the alleged fight against crime and corruption," Dodik said.
Dodik, a critic of the West who favors closer ties with Russia, accused the central Bosnian government of conspiring with USAID in the matter and said that NGOs in the Serb Republic which receive USAID funding would be investigated.
Bosnia is divided into a Serb Republic and an entity for its Muslim Bosniak and Croat populations, which are linked via a weak central government.
The U.S. Embassy dismissed Dodik's accusations.
"Once again, the assistance of the people of the United States is being used to support wild conspiracy theories in the interest of election campaigning in Bosnia," it said in a statement.
The embassy said it was still negotiating with the Bosnian central government programs worth a total $8 million to help combat graft, and it accused Dodik of trying to mislead the public and intimidate USAID partners.
Bosnia's Prime Minister Denis Zvizdic also dismissed Dodik's allegations, saying the programs accepted by the Council of Ministers were only at an initial stage and could not influence the election process.
Dodik, who has been blacklisted by the United States for pushing for an illegal referendum on an illegal holiday, has often accused Western governments of being biased against Serbs.
Political analysts said Dodik's rhetoric showed he had begun early campaigning for Bosnia's parliamentary and presidential elections on Oct. 7. He plans to run for the Serbs' seat in Bosnia's tripartite inter-ethnic presidency.
Last month, Dodik also accused Britain of sending intelligence specialists to Bosnia to meddle in the election campaign. Britain said he was "inventing fake threats" as part of his election campaigning.
(Reporting by Daria Sito-Sucic; Editing by Gareth Jones)