Mr Jones was unrepentant this afternoon.
"Is this the same Green Party that complains of Colin Craig being too thin-skinned?" he said.
"I'm from Kaitaia. I know it's mollyhawk in the north. Further down the line it's mollymawk. Now I could've got my names wrong but people should just loosen up.
"The thought that it's led to a complaint, I'll just leave the public to judge that for what it is."
Mr Jones said Mr Hughes was not respecting the role of an independent state body.
He accused Mr Hughes of undermining the Environmental Protection Agency (EPA) as it heard submissions on mining iron ore off the west coast of the North Island.
Mr Hughes had urged the EPA to take into account all of the 4800 submissions, the vast majority of which were against iron ore extraction.
Mr Jones said he had agreed to stay out of another independent agency's inquiry - the Commerce Commission's investigation into alleged extortion by the supermarket industry - and Mr Hughes should do the same.
Mr Spagnolo said that he spoke with Labour's chief of staff regularly but complaints were rare.
"It's an informal complaint... it's petty stuff."
Labour leader David Cunliffe did not think that Mr Jones' comments warranted an apology.
"We're fortunate with Shane that he has a colourful turn of phrase... but on occasion his oratory crosses the line into something he might want to consider."
He also warned Mr Jones about treading on other colleagues' portfolios at a University of Auckland debate last week.
Mr Jones has repeatedly attacked Greens about its stance on mining and fisheries.