Supporters and fellow rights activists said the fine - equivalent to USD 18,300 or 16,150 euros - is believed to be the largest ever imposed on a Russian organisation for violating the notorious law and comes ahead of parliamentary polls in September.
Following unprecedented protests against his decade-long rule, President Vladimir Putin in 2012 signed off on a law that requires non-governmental organisations which receive foreign funding to register with the authorities as "foreign agents".
Grigory Melkonyants of Golos said the organisation had been fined following a request from the justice ministry because some materials posted on its website did not carry an appropriate tag.
Golos representatives had not been invited to take part in a court hearing last week, Melkonyants added, saying that their lawyer would contest the decision.
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He said Golos had asked the justice ministry three times to remove it from a list of foreign agents but had been refused every time. The vote monitor has been repeatedly harassed and fined in the past.
"It is obviously a directive from the above," he said, referring to a decision to slap the fine on the monitor.
"The authorities are preparing to commit falsifications. Why do they need anyone to watch over them?"
The September elections come as Russia is facing a prolonged economic crisis due in part to the plunge in oil prices and Western sanctions over the Kremlin's role in Ukraine.
Putin has warned that "foreign enemies" were seeking to disrupt the elections and tasked the FSB security service with preventing any interference.