Voters could no longer cast ballots "against all" and in most regions there was no longer a minimum turnout required to validate the election.
In a few regions, all voting was by party, meaning no ballots could be cast for individual candidates and parties had to clear a higher minimum threshold of seven per cent to gain seats.
Candidates from 14 parties competed in the regional polls which critics say do not represent genuine pluralism.
The Gazeta newspaper said: "The election process overall has become meaningless in its present form.
"The amount of falsification, black PR, open criminality, pressure and threats to opponents was simply too great."
Barred from ballots
Garry Kasparov, who leads the Other Russia opposition movement, said: "Russia today technically is a police state and this corrupt and unethical Putin regime is trying to survive at any cost.
"They know that with free and fair elections and no censorship they will not last long,'' the former world chess champion said.
Voters in St Petersburg were dismayed that some parties had been barred from the ballot.
Yabloko, a liberal party, was excluded by a ruling that more than 10 per cent of the signatures it gathered to enter the race were invalid.
Another party, the liberal Union of Right Forces, was barred from the ballot in four regions because in some cases candidates withdrew under pressure from threats or with promises of jobs, its leader said.
Over the weekend, police in St Petersburg dispersed one of the largest opposition rallies in Russia in years, mainly complaining against the sidelining of opposition parties.