Reactors 1 to 4 were declared defunct in April, 2012, 13 months after the devastating 2011 earthquake and tsunami.
That leaves Japan with just 48 operable nuclear reactors, all of which remain offline, pending safety checks after the Fukushima nuclear power plant disaster.
"With the decision to decommission the two units, the whole power station will now be decommissioned," Tepco said in a statement Wednesday. "We feel an overwhelming sense of shame and regret at the fact that by this accident, we have failed to repay the trust placed in us by the local residents," the utility said.
The entire 6-unit facility had a total output 4,696 megawatts.
Last month, Tepco started the delicate operation of removing more than 1,000 nuclear fuel-rod assemblies from the spent fuel pool inside the damaged No. 4 reactor building. The utility expects to complete that process by the end of 2014.
But the overall decommissioning work at the stricken nuclear plant is expected to take as long as 40 years.
When Prime Minister Shinzo Abe visited the Fukushima site in September, he urged Tepco to scrap reactors 5 and 6, so the utility could focus more on the crisis cleanup efforts.
Units 5 and 6, which had been under "periodic inspection" when the massive earthquake occurred, "were able to achieve cold shutdown since their emergency power source was functional" and had escaped major damage, Tepco said Wednesday.
Tepco said it is considering using the two units as a research and testing ground "for remote decontamination of the inside of reactor buildings, investigation of the inside of primary containment vessels and equipment to remove fuel debris."
The utility said it was discussing that plan with manufacturers and research institutions, noting that such a plan was "for the purpose of steadily implementing the decommissioning work at Units 1 to 4, with its unique and highly technical challenges."
Tepco said it was studying the financial repercussions of its decision to decommission Units 5 and 6.
Separately, the Asahi Shimbun newspaper reported Thursday that the Japanese government is set to offer additional financial assistance to Tepco for the Fukushima disaster, increasing the cap on interest-free loans through the state-backed Nuclear Damage Liability Facilitation Fund to $87 billion from $48 billion.
"The roles of the government and Tepco will be clearly defined to advance rehabilitation of Fukushima without delay," the newspaper cited a draft of government guidelines for accelerating recovery from the nuclear accident, as stating.