Anatoly Ledovskikh said TNK-BP has failed to manage its licenses properly, and the agency cannot prolong them despite the company's repeated requests.
"We cannot transfer terms mentioned in the licenses from 2001 to 2009. All should be done on time," he said adding that TNK-BP has this possibility.
With 1.9 trillion cubic meters of proven reserves, the 62.4% TNK-BP-owned deposit is crucial for the Russian government, which is pursuing ambitious plans to build a gas pipeline network to meet Asian nations' energy needs, primarily energy-hungry China, and to diversify its export destinations.
Ledovskikh said TNK-BP is facing transport problems because it expected Russian energy giant Gazprom to allow the company to use its pipeline instead of building its own.
"I hope they will finally reach an agreement," he added.
Gazprom, which was appointed in 2001 to coordinate all gas projects in East Siberia and Russia's Far East, said in early December it might join the Kovykta gas project in East Siberia.
The two companies discussed a cooperation project to build a unified network for upstream and downstream operations, and gas transportation in East Siberia and the Far East.