The old, single education portfolio will now be split into three different parts.
Peter Garrett will take over schools, Kim Carr is to oversee postgraduate education, while Chris Evans is to be responsible for Labor's school building program, undergraduate university and vocational skills.
Mr Pyne said dividing the portfolio was a major mistake.
"It is an error on the government's part, I think they have dropped the ball again," he told the Macquarie Radio Network on Monday.
"They should act to fix it - obviously we need to have a minister for education."
The nation's universities did not expect to be regarded as a skills factory or a jobs factory, Mr Pyne said.
Labor may have deliberately split the portfolio into three in a bid to avoid scrutiny, he said.
"This makes it harder for the government to be held to account if you don't know who to go to to complain."
The move would not make the handling of federal education issues any more efficient, as there were natural "synergies" between primary, secondary and higher education.
Having Mr Garrett, the minister who rolled out the bungled home insulation scheme, in charge of educating children was another "frightening" result of the reshuffle, Mr Pyne said.
He flagged the coalition would move for a judicial inquiry into the Building the Education Revolution scheme through a private member's bill in parliament.
"That will be one of the first tests of the independents, the Greens and Andrew Wilkie in the House of Representatives."
