Jack Straw has said departments should not be reorganised based on the "whim" of prime ministers and advice of "earnest young Turks" in 10 Downing Street.
The former justice secretary called for reform after admitting that senior judiciary were "discombobulated" by the way they found out about plans for the creation of the Ministry of Justice.
Straw said he believed re-organisation of central government departments and arm's-length bodies should be set out in advance and given "proper examination".
The former cabinet minister, who served as home secretary and justice secretary under Labour, told MPs on the Commons justice select committee that the creation of the Ministry of Justice in 2007 had brought benefits and had been "inevitable".
But he said he did not approve of the way in which "machinery of government" changes were made.
"I think it is too capricious, it is too informal and it is too much at the whim of whoever is prime minister," he told MPs.
"There are sometimes good reasons for making changes, but if there are good reasons then there is no earthly argument why those reasons should not be set out in advance and subject to proper examination before the decision is made."
He added that senior judiciary had felt "blindsided" when they were told of the plans for the creation of the Ministry of Justice.
He added: "Senior judiciary, as I am sure is widely known now, were extremely discombobulated by the way they found out about the proposals for change, and I don't blame them, because they were effectively blindsided about them."
Asked if he believed the judiciary did not have much input into the creation of the new department, Mr Straw said: "I wasn't there at the time, but if you ask them, they will say that they found out about the plans whilst on a residential conference and that was obviously not an appropriate way for them to find it out.
"It goes back to this issue of the way in which machinery of Government changes have been handled.
"Because it is in the hands of the prime minister, what happens is you get a very small unit in the Cabinet Office and often some earnest young Turks in Number 10, who have a bright idea about how the Government's problems will be solved if they change this department or that department and there isn't any proper check on it."
He said: "My fundamental point is that the institutions of Government, the departments, should not be seen as being owned by the prime minister of the day.
"These are national institutions."