A Tauranga Destiny Church pastor charged after allegedly organising two protests while the city was under Covid-19 gathering restrictions has pleaded guilty, but whether or not he will be convicted is yet to be determined.

Leon Wharewehe Samuels, 46, originally faced two charges of failing to comply with an order issued under Covid-19 Public Health Response Act, relating to what police allege was his role in organising protests against Covid-19 restrictions.

Those two protests were held at Tauranga parks while the region was in Alert Level 2 restrictions in October last year.

The first protest happened on October 16 - the same day as the nationwide 'Super Saturday' vaccination campaign. Police alleged Samuels was responsible for the event, which saw 400 mainly unmasked attendees congregate at Coronation Park.

A similar charge was laid relating to a protest also allegedly organised by Samuels at Memorial Park on October 30. He had previously pleaded not guilty to both charges.

Supported by family, Samuels appeared for his Judge-alone trial at the Tauranga District Court on Thursday dressed in a black shirt and suit.

But the trial never went ahead; when Samuels was called, lawyer John Wayne Howell informed Judge Bill Lawson that an agreement had been reached with the police to withdraw one of the charges. A guilty plea was entered for the remaining charge.

Howell told the judge his client was seeking a discharge without conviction - a proposition the police prosecutor indicated he was likely to take a "neutral position" on.

That matter is set to be discussed when Samuels reappears for sentencing on June 9.