Neil Basu of Met police says half of force's armed officers could stop carrying weapons if barred from conferring on statements

A police chief has said more than half of his force's armed officers could stop carrying weapons because of plans by the police watchdog to ban them from conferring with each other as they write up statements following a shooting.

Commander Neil Basu, Scotland Yard's head of armed policing, said the Independent Police Complaints Commission was being driven by a desire to salvage its battered reputation. He said the plan would leave officers feeling "criminalised" as murder suspects for doing their duty in tackling gun crime.

He said officers were likely to withdraw cooperation from investigations into the police following shootings and give "no comment" answers to any questions.

Basu's comments in a Guardian interview brings into the open a seething row between the police and its watchdog. The IPCC is acting after years of criticism over officers sitting with each other and conferring after serious incidents as they write up their statements. The police say conferring covers only the lead-up to the use of force. Critics including the high court say it is an opportunity for collusion.

Basu said the IPCC was pandering to a small minority who believed marksmen were "liars" conspiring to hide the truth by conferring. "I think that is based on the perception that officers confer to lie," he said.

Basu said he feared that 50-65% of his force's armed officers would decide not to carry a weapon any more. "I think there is a very serious risk that officers will no longer volunteer for the role." More than 2,000 officers in the Met carry arms.

Basu said his officers opened fire rarely and showed professionalism and restraint. "This is not … about paramilitary policing and death squads," he said.

Under the IPCC plans, which cover all forces in England and Wales, officers would be separated from each other where practical after serious incidents such as a shooting, use of a Taser stun gun or a death in custody.

Officers would not be allowed to talk to each other at any stage before or while writing up their account, according to the IPCC's proposals, which the watchdog is consulting on. They would also be expected to write their full account before going off duty, instead of the current system where they have 48 hours to recover.

The police say the current system means IPCC investigators get the "best evidence" available.

The IPCC announced the proposals to stop the practice of conferring after the inquest into the shooting of Mark Duggan. A jury found he was unarmed when shot dead but that the armed officer acted lawfully because he believed Duggan was holding a weapon. Days after the shooting, police officers sat in a room together for eight hours writing their accounts.

Basu said a leading lawyer for armed officers had warned that they would refuse to answer questions from the IPCC if the watchdog insisted on separating them after shootings.

"No amount of fantastic Churchilian leadership from me is going to make an officer want to contribute to an inquiry where they are being made a suspect," he said. "They will be legally advised to make no comment. Why wouldn't they, knowing that the slightest mistake they make … and they are potentially facing a murder charge for doing their job?"

Basu said separating officers after an incident as traumatic as a shooting would increase their stress, leaving them isolated at a time of their greatest need.

A survey of firearms officers released last week found that eight in 10 lacked confidence in the IPCC's planned changes and two-thirds in the Met "would think seriously" about handing in their weapons if the changes went ahead. Nine out of 10 believe that having to make a full statement after an incident – without having 48 hours to recover – would add to the stress they face and say the changes would make them feel like a criminal suspect.

Officers are already warned not to confer about why they may have used force and the actual use of force.

Basu said claims that the police and IPCC were too close were "laughable", and said the watchdog was fighting for its survival.

The IPCC's director of investigations, Moir Stewart, a former senior Met officer, said separating officers where practical gave the public better reassurance.

"It adds integrity to their accounts and protects them from accusations of a cover-up or collusion," he said. "I believe that explainable inconsistencies are more credible than unexplainable consistencies. The proposals we have put forward as part of our draft guidance will increase public confidence in the police version of events, and help ensure our investigations are as robust and thorough as they can be."

The IPCC said it would consider the police service's views, and it would be up to home secretary, Theresa May, to decide whether or not to approve the proposed statutory guidelines.