Sergei Simakov, a district councillor from Ussuriysk, said: "We had hoped good sense would prevail ... This could disrupt the economy and bring many problems".
At Moscow's large Dorogomilovsky market, some stalls had been forced to close and were displaying signs reading: "Wanted: Sales-people, must be Russian."
In other cases foreigners remained in behind-the-scenes roles but had hired locals to trade on their behalf.
The government order announced last November and effective from April 1 bans foreigners from conducting transactions at market stalls, although they are still allowed to own such stalls.
Up to 12 million foreign nationals are believed to work illegally in Russia.
Price rises
A spokesman for the federal migration service, Konstantin Poltoranin, promised that enforcement would be carried out in an orderly fashion.
"This doesn't mean that from April 1 we will start large-scale raids and special operations. We view this date calmly and will check compliance with migration legislation ... as we did before," Poltoranin was quoted by Russia's Interfax news agency as saying.
Sergei Darkin, the governor of the Far Eastern province of Primorsky, said he was concerned about the possibility of price rises.
"We should do all we can to ensure reasonable prices for imported goods that meet the demands of our province's consumers. This demand can't be met just by native producers," Darkin said.