A senior undercover police officer took backpacks containing secret equipment from slain colleague Sergeant Don Wilkinson because he didn't want them falling into the wrong hands - including those of other police.

A High Court at Auckland jury has heard the officer, who has name suppression and can only be identified as Officer W, took the backpacks from the scene soon after Mr Wilkinson and his colleague were shot.

The shooting happened during a covert operation to place a tracking device on a car outside an alleged P manufacturer's house in Hain Ave, Mangere, on September 11, 2008.

John Ward Skinner, 37, and Iain Lindsay Clegg, 33, are charged with Mr Wilkinson's murder and the attempted murder of the other officer. Skinner is also charged with assault with a firearm.

Both men are defending the charges.

Officer W told Skinner's lawyer, Kevin Brosnahan, he removed the bags because if the content of them were known it could have "national or even international ramifications".

Mr Brosnahan said Officer W was "a very senior and experienced officer...[But] you breached the golden rule, the most basic rule of crime scene investigation [not to remove items from a scene]".

Officer W replied he chose to breach that rule over a rule of his unit. "I chose to preserve the integrity of the equipment in those bags," he said.

Mr Brosnahan challenged Officer W's reasons for taking the bags in the aftermath of the shooting, telling him there was "no risk" they could have fallen into anyone else's hands.

Officer W took the bags and placed them in his car while there were only police and ambulance staff present and no scene examination had occurred.

Officer W replied, "I wouldn't even be happy with them falling into the hands of other police."

Mr Brosnahan accused him of compromising the integrity of the crime scene and of giving conflicting statements on the night's events.

The witness agreed he took the bags "without saying a word" to anyone and that the court relied now only on his word on what was inside them.

"That's why I'm here today giving evidence."

Earlier in the week Officer W gave evidence he and Sergeant Wilkinson believed the rendezvous point to go to if the operation went wrong was in a different location than where other police involved in the mission thought it was.

Mr Brosnahan today put it to him that belief was "invented after the event" to cover the fact Mr Wilkinson and the officer went to their car, instead of going to the agreed rendezvous point.

Officer W said that was "emphatically incorrect". He also denied calling 111 after finding Mr Wilkinson dying on the road. He said he made the call only after the officer-in-charge of the operation called him to say what happened.

He walked past Mr Wilkinson and the other officer, who can only be known as Officer M, to get to his car and didn't see them lying injured in the dark.

Officer W's evidence is being given in a closed court with only police and reporters present. Suppression orders have also been imposed that restrict reporting aspects of Officer W's evidence.

The trial continues.