The tax claim had challenged most of those payments as dividends.
The settlement also took care of a $165 million tax claim.
Investors following the dispute said that the new 2001 tax claim was not unexpected.
The army has seized property worth many times the tax claims.
It said the plan failed to take the tax claim adequately into account.
They started the criminal case, the tax claims, to show to others what can happen to them.
Yukos, which produces 2 percent of the world's oil, said it would continue to fight the 2001 back tax claim.
Yukos is paying off a $7.5 billion tax claim for the years 2000 and 2001.
The tax claim was contested and eventually accepted in 1993.
The company underscored that the tax claim was only a first notice.