A ban on Borjomi would be effective May 7, while Nabeglavi would be prohibited starting May 10, Gennady Onishchenko said.
The ban on Nabeglavi follows the suspension of Borjomi imports that Onishchenko announced Thursday, citing numerous documentation problems that made it difficult to tell genuine Borjomi from illicit copies.
The move came only six weeks after a ban on Georgian wine imports for reported health safety reasons. The wine ban was later extended to cover cognac and sparkling wine.
Onishchenko instructed regional customs services to suspend supplies of Borjomi and Nabeglavi starting from the given dates.
"[Checks] have exposed large batches of Nabeglavi that do not correspond to mineral water requirements, including calcium, chloride, magnum, and permanganate oxygen," Onishchenko in a letter to the Federal Customs Service and the Federal Service for the Oversight of Consumer Protection and Welfare.
Onishchenko sent a similar letter about Borjomi on Thursday, but did not specify in it the timeframe for the ban.
Wine and mineral water are two of the South Caucasus republic's biggest exports, and the March ban on wine increased tension in already strained relations between Moscow and Tbilisi.
Onishchenko said 175,560 bottles of Nabeglavi had been found to be in breach of content requirements in the past week.
Borjomi is a salty sparkling water from mineral springs in Georgian mountains. Its producers say it is good for people with liver, kidney and digestion problems. The company controls about 10% of the Russian mineral water market.
Onishchenko said he suspended the already issued licenses and state registration documents for Nabeglavi and Borjomi until experts establish the reasons behind the violations.