The decision came amid an ongoing conflict between the British oil major and its Russian billionaire shareholders. The four Russian tycoons have sought Dudley's dismissal and accused him of acting only in BP's interests.
The BP-appointed U.S. executive said he was leaving due to the failure of the Russian authorities to renew his visa. A transit visa issued for Dudley expires next Tuesday. Migration authorities said Dudley needs to provide a valid employment contract instead of the one that expired late last year. TNK-BP have said that Dudley's contract is open-ended.
Dudley said the uncertainly was extremely "destabilizing" for his work and the company's operations.
"BP is deeply disappointed that Mr Dudley has reached the conclusion that the interests of TNK-BP would be best served if he performed his duties outside Russia," the firm said on its website.
BP also regretted "the continuing harassment" of Dudley by the Russian "Alfa, Access and Renova (AAR) shareholders".
The company has been hit by a wave of tax, labor and police inspections along with visa problems since March. BP has accused its Russian partners, who hold the other 50% in Russia's third largest oil producer, of employing raider-like tactics in pursuing control of TNK-BP.
Dudley said he hoped the pressure on the company would ease after his departure.
On Wednesday, a Siberian court ruled the temporary appointments of foreign technical staff to TNK-BP by BP were illegal. It upheld complaints by minority shareholder Tetlis that the use of 148 secondees cost the venture about $150 million a year, which amounted to an additional dividend to BP. The British oil major denied the allegation.
The ruling came after BP had announced the withdrawal from Russia of all 148 of the company's foreign technical staff.
TNK-BP said on Thursday that Dudley would remain the company's general director and management board chairman and would retain the authority to run the company.