Anatoly Beskorovainy, an aide to the general director of the Atlas research center, known as the developer of Russia's Unified State Automated Information System (EGAIS), said the center started working on the system in 2005 using its own resources.
The Federal Tax Service was supposed to pay for the development but never did, he said.
The system is part of new alcohol production and distribution regulations introduced by the Russian government to prevent bootleg wines and spirits from entering the market.
Beskorovainy did not say how much the FTS was to pay his company, but a Kommersant source estimated the development of software for the system at $10-20 million.
The FTS was put in charge of EGAIS last June. Prior to that, the system's development was overseen by the Federal Security Service (FSB).
In November, Prime Minister Mikhail Fradkov issued an order placing Atlas under the Industry and Energy Ministry.
But Beskorovainy said none of these agencies have signed any formal agreements with the center on EGAIS and therefore, EGAIS modules, already installed at distilleries, are Atlas's intellectual property that it may in theory dismantle if it is not paid.
FTS Press Secretary Aelita Baichurina declined to comment on Atlas's claims.
Legal experts said that should Atlas decide to take the matter to court, it would not have much chance of winning.
In late August, the deadline by which alcohol producers and sellers will have had to submit data to EGAIS was postponed from November 1 until further notice.
Russia's Unified State Automated Information System will receive data from devices measuring the volume and alcoholic content of beverages. Installation of the counters at all companies producing and selling alcohol, excluding retailers, will be compulsory.
Earlier, a government source said that the deadline had been moved to June 1, 2008.
In late June, Russia's Federal Tax Service restored licenses to 121 alcohol producers who had their operations suspended earlier that month in a regulatory dispute.
Some 320 companies had their licenses revoked in early June following non-compliance with a law requiring all producers of alcohol to install automated alcohol meters by May 1, the source said.
Most of the suspended businesses were small or medium-sized companies, with a combined output accounting for just 10% of the nation's total sales, so their temporary suspension had not caused any major supply shortages.
Industry analysts said the failure to comply with the new regulations resulted from a widespread belief that EGAIS would not work.
The tax authorities planned to start loading data from producers' automated alcohol meters into EGAIS on February 1, 2007, but the government conceded in January that EGAIS was not operating properly, and moved the startup date to November 1, 2007, setting a deadline of May 1 for the installation of the automated meters.
Last year, the Russian government ordered all alcohol retailers and distributors to sell alcohol with new excise tax stamps, but failed to start up EGAIS as planned and to print enough stamps, causing severe shortages of alcohol on the consumer market.
