Maharey is chair of drug-buying agency Pharmac, ACC and Education New Zealand and is subject to a code of conduct requiring him to remain politically neutral.
A former Cabinet minister for Helen Clark's Labour government, he also writes a regular opinion column for Stuff.
The spotlight has fallen on politicised comments he made in the column after the summary firing of Rob Campbell from chairing roles at Te Whatu Ora (Health NZ) and the Environmental Protection Authority last week.
In a statement on Wednesday afternoon, Hipkins said advice from Public Service Commissioner Peter Hughes found Maharey had breached the code of conduct, but his actions did not justify his removal from his roles.
"The Commissioner has characterised Mr Maharey's actions as 'unwise', but at the 'lower end of the spectrum'," Hipkins said.
He said there was a "clear distinction" between Maharey's breach and Campbell's.
"In Mr Maharey's case, he proactively acknowledged the error, has undertaken to stop writing the column and apologised," Hipkins said.
"Based on this advice, Ministers Ayesha Verrall (Health), Jan Tinetti (Education) and Peeni Henare (ACC) have confirmed this morning that they retain confidence in Mr Maharey and will keep him in his roles."
Another former Labour MP, Ruth Dyson, was pulled into the crackdown on political neutrality by public servants this morning after the National Party questioned a tweet she had made criticising Luxon's speech at Waitangi.
Dyson, the deputy chair of the Earthquake Commission and Fire and Emergency New Zealand, admitted she had not read the code of conduct, but said she was rethinking her social media use in light of Campbell's sacking.
Hughes also told MPs he would contact all Crown entity board chairs and reiterate the impartiality requirements after Public Service Minister Andrew Little requested it.
Hipkins on Tuesday afternoon said the principle of political neutrality was long-standing, but was only laid down in the code of conduct as a core principle last year.
"Where other potential breaches are brought to light, the responsible minister will need to consider these individually, with support from the Commissioner.
"However, particularly when they are historical and are at the lower end of the spectrum, my guidance to ministers is that provided the person acknowledges and regrets the breach and is clear about adhering to the code going forward, it should not necessarily result in the responsible minister losing confidence in them.
"No one is perfect, but it's only right that board chairs and members understand the bounds of what they can say without jeopardising their ability to perform their roles."
Hipkins said there were excellent people in public roles, including former National and Labour MPs, and "no one thinks they don't or shouldn't hold their views" - but the roles came with obligations to exercise caution and discretion.
