The strike follows a call by union leaders for controllers in 45 of Russia's 89 regions to join the protests, after they rejected a 15% pay increase on Saturday.
"
Planes will fly, and people will strike. This is a
sign of democracy
"
Dmitry Ayatskov, Governor of Saratov
The strike could affect air travel across the country and cause delays and cancellations to flights between Europe and Asia.
Earlier this month several hundred air traffic controllers stopped taking food but continued to work, as part of a demand for a 30% rise from their current monthly salary of 15,000 roubles ($470).
Under Russian law, air traffic controllers are not allowed to refuse to work, as they are judged solely responsible for air safety.
Low wages: spiralling costs
The strike is so far confined to Siberia, with workers in other parts of Russia largely ignoring the union's calls for action.
Unlike their counterparts in high-profile airports in Moscow and St Petersburg, Russia's provincial air traffic controllers suffer the same sort of low pay and wage arrears as other state and municipal employees.
But cities in oil-rich Siberia have seen living costs spiral in recent years, and the average wage in the Tyumen oil region is now more than 12,000 roubles a month, one of the highest in Russia.
Sunday's planned strike has received a seemingly casual response from some Russian officials.
"Let them strike," said Dmitry Ayatskov, governor of the central region of Saratov.
"Planes will fly, and people will strike," he added. "This is a sign of democracy."
Government officials disagreed with union leaders over how many regions had been affected.
Sergei Kovalyov, president of the Air Traffic Controllers Union, said 30 workers had begun to strike on Saturday and their numbers were expected to double, the Interfax news agency reported.
But Valery Yezhov, from the state organisation that oversees Russia's air controllers, said flights had not been affected at all on Sunday.
"I do not expect the situation to grow worse on Monday either," he told the Tass news agency.