He said the district health boards and public health units should have communicated the changes to both him and the public and he'd be speaking with them in the next few days.
RNZ reported this morning there are just now just six community testing sites still operating - down from 20 at the peak of the second Covid-19 outbreak - with none open over the weekend.
Hipkins said fixed community sites had lower testing rates with some as low as just 26 tests over one weekend.
"That's very resource intensive - that's a lot of people standing around to do not very much testing."
Whereas pop-up sites, for example in a supermarket carpark, get much higher testing rates.
"So that's one of the things we need to look at, whether we need to be moving the testing sites around more frequently because we know when we move them around we get a higher degree of people using them."
But Hipkins said those changes had not been communicated to him or the public and he would be following it up.
"The closure of those testing sites was not something I was consulted on and clearly I think there was a communication challenge there the relevant people didn't work through well enough," Hipkins said.
"I don't think there was any ill-intent here. I think they were looking at how to best use the resource and that's the right question to ask.
"But I think there's a communication challenge here to make sure that we're communicating changes we're making."
Director general of health Ashley Bloomfield also told RNZ he would be speaking with the health boards to make sure testing centres were accessible as necessary.
Hipkins said he would be talking with the relevant people over the next few days to make sure it was sorted by the weekend.
"One of the key measures here is everybody should be able to get a test when they want a test and they need to know where to go to get a test so if the community testing sites are being shifted then people need to know where they could go instead."
People are still able to get tests at GPs.
In the first instance anyone with symptoms should always call Healthline first as they would be able to advise where tests were available, he said.
In light of the latest community case of a marine electronics engineer who tested positive after working on a ship now bound for Brisbane, Hipkins said he was reviewing whether people who come into New Zealand to transit directly onto a ship also need to be tested.
But there were logistical challenges and safety concerns for sending people out to test people on ships who might never actually come ashore, he said.
For people coming ashore, there was testing available.
The Maritime Union has called for foreign seafarers to be tested as well.
Hipkins said all of the case's contacts had been quickly identified, isolated and all so far had returned negative tests which would suggest it was well-contained.
The engineer had been tested four times - roughly every fortnight - and was due to be tested again before they sought a test for having mild symptoms.
"This appears to be a textbook case of how the system should work."
