The legal action follows complaints from Russia's largest fertilizer producers EuroChem and PhosAgro, Prime reported Tuesday.
A representative for the FAS said that if found guilty the company faces a large fine.
The maximum penalty for anti-competitive conduct can reach up to 15 percent of the company's turnover, Prime reported.
Gazprom claimed that their pricing depends on the global market prices of sulfur and diammonium phosphate, as well as other variables.
The FAS dismissed the claim by saying that neither the diammonium phosphate price nor the global pricing structures can be transferred directly to Russia's domestic market.
This is not the first anti-monopoly case against Gazprom.
According to the FAS, in March 2011, the price on liquid sulfur jumped 246 percent from the previous month and continued to grow throughout the year.
In June 2012 the company's pricing formula was deemed unlawful based on article 10 of Russia's competition protection law. The company was fined 17.5 million rubles ($532,000) but is currently appealing the decision.
Most of Gazprom's sulfur is produced in the Astrakhan and Orenburg regions. More than two-thirds of the sulfur produced in Russia is exported. The chemical industry accounts for 76 percent of domestic sulfur consumption, Interfax reported.
A Message from The Moscow Times:
Dear readers,
We are facing unprecedented challenges. Russia's Prosecutor General's Office has designated The Moscow Times as an "undesirable" organization, criminalizing our work and putting our staff at risk of prosecution. This follows our earlier unjust labeling as a "foreign agent."
These actions are direct attempts to silence independent journalism in Russia. The authorities claim our work "discredits the decisions of the Russian leadership." We see things differently: we strive to provide accurate, unbiased reporting on Russia.
We, the journalists of The Moscow Times, refuse to be silenced. But to continue our work, we need your help.
Your support, no matter how small, makes a world of difference. If you can, please support us monthly starting from just $2. It's quick to set up, and every contribution makes a significant impact.
By supporting The Moscow Times, you're defending open, independent journalism in the face of repression. Thank you for standing with us.
Remind me later.