The official, Andriy Yermak, who leads Kyiv's negotiating team trying to hash out terms after Washington presented a draft backing Russian demands, confirmed his apartment was being searched and said he was fully co-operating.
In a joint statement, the National Anti-Corruption Bureau of Ukraine and the Specialised Anti-Corruption Prosecutor's Office said the searches were "authorised" and linked to an unspecified investigation.
Earlier this month, the two anti-corruption agencies unveiled a sweeping investigation into an alleged $US100 million kickback scheme at the state atomic energy company that ensnared former senior officials and an ex-business partner of Zelenskiy.
Yermak, 54, has been a close friend of Zelenskiy since before the one-time sitcom star embarked on his political career, and helped guide his 2019 presidential campaign.
He has not been named a suspect, but opposition politicians and some members of Zelenskiy's own party had called for his dismissal in Ukraine's worst wartime political crisis.
Friday's searches are likely to inflame tensions between Zelenskiy and his political opponents as Kyiv faces mounting pressure to accept a deal that could force it into painful concessions.
In a statement, the European Solidarity opposition party criticised Yermak's role as a negotiator and called on Zelenskiy for "an honest dialogue" with other parties.
"The president should not limit himself to comfortable communication with his faction - he is obliged to explain to the entire parliament... what directives and 'red lines' were given to the Ukrainian negotiating team," it said.
The US-backed peace push comes as Russian forces grind forward along several parts of the sprawling front line. Moscow says its troops are close to capturing the eastern city of Pokrovsk, which would be their biggest prize in nearly two years.
Speaking to The Atlantic magazine this week, Yermak said "no one should count on us giving up territory".
Political analyst Viktor Shlinchak, of the Kyiv-based Institute for World Politics, described the searches as a "Black Friday" for Yermak and suggested Zelenskiy may be forced to dismiss him.
"It looks like we may soon have a different head of the negotiating team," he wrote on Facebook.
