Kerala police maintained that no rifles were missing, a day after the CAG audit found shortage of 25 INSAS rifles and 12,061 live cartridges from the Special Armed Police Battalion in Thiruvananthapuram.
Meanwhile, the opposition Congress and BJP slammed the state government on the issue and demanded action against the police chief.
"Twenty five INSAS rifles were reportedly missing as per the CAG report. The crime branch investigation conducted so far has revealed that no INSAS rifle is missing as on today.
"The Crime Branch is once again doing a physical cross verification of all the weapons issued to the Special Armed Police (SAP). Investigation is going on to trace the missing rounds," a statement from the state police media centre said on Thursday.
The Comptroller and Auditor General of India report had stated that 12,061 live cartridges were found missing in a joint verification in the Bell-of-Arms of SAPB, along with the Assistant Commandant.
The CAG had come down on state police chief DGP Loknath Behera for purchasing bullet-proof vehicles for VVIP security, violating guidelines.
There was shortage of 250 9 mm Drill Cartridges, which was "covered up" with dummy cartridges, the report on General and Social sector for the fiscal ending March 31, 2018 had said.
Slamming the LDF government, Minister of State for External Affairs V Muraleedharan said the allegations against the DGP and state police had put Chief Minister Pinarayi Vijayan on the defensive as he heads the home department.
"Does it mean the CM was unaware of the matters? It needs to be found out whether these missing rifles and ammunition had been handed over to the extremist outfits," he wrote on his Facebook page.
Attacking the government over the CAG report, Kerala PCC President Mullapally Ramachandran demanded the resignation of Vijayan and DGP Loknath Behera.
"Both the Chief Minister and State police chief should resign and face action," he said.
He alleged that a CBI probe will not bring out the truth as Behera was close to the Narendra Modi government.
Leader of the Opposition in the assembly Ramesh Chennithala wrote to the Chief Minister, demanding removal of Behera from the post in the wake of serious allegations levelled against him and the police department in the CAG report.
In his letter, the senior Congress leader said a CBI probe against Behara and a NIA investigation into the missing rifles and cartridges need to be conducted.
Meanwhile, Behara also met the Chief Minister at the Secretariat.
The DGP is expected to leave for the UK in the first week of March to attend a conference, police sources said.