The petition alleged a "high-level political conspiracy in the murders".
"In some cases, party activists from the constituency of the present Chief Minister, who is holding the home portfolio, are involved," the petition read. "These facts and circumstances clearly indicate high-level political conspiracy in planned execution of the murders and the efforts to hide the real culprits."
The petition was filed on Tuesday as the BJP ended its 15-day foot march across the state to highlight what it said was the "murder politics" of the CPM.
The yatra had started near Kannur, the epicenter of the political violence, where, the BJP says, 14 men of the party and the RSS had been killed since the LDF government came to power in May 2016.
Launching the foot march two weeks ago, BJP chief Amit Shah had said CPM chief minister Pinarayi Vijayan was "directly responsible for all political murders in Kerala".
Government data shows since the Left government was voted to majority, there have been 16 political murders - four of the victims were CPM cadres and eight belonged to the BJP and the RSS.
On Sunday, top BJP leader Saroj Pandey had told the media that BJP's Jan Raksha Yatra was to get a message across to the CPM workers that if they even looked at the BJP workers, "we will enter their homes and gouge their eyes out".
The CPM has also been conducting counter-protests against the BJP violence in Kerala and other parts of India. The party, led by general secretary Sitaram Yechury, is holding a protest march against the BJP in the national capital today.