Home secretary John Reid announced that the Home Office will split on May 9th, with the Department for Constitutional Affairs becoming the new justice ministry.
But Lord Woolf, who retired from his position in October 2005, warned on the Today programme that "we should be more careful about how these matters are dealt with".
"We have no written constitution which is entrenched, and our constitution works through checks and balances," he said.
"And it's very important that if we are starting to alter the framework of checks and balances, that the matter's looked at carefully.
"I'm not saying that it can't be made to work satisfactorily; what I am saying is that we should work it out beforehand and not wait until we've created the change and then somehow or other try to scramble to get it in place."
And he stressed that it was "a very big change" to the constitution.
"I say it for no other reason than that I am concerned for our wellbeing as a nation," he said.
Lord Woolf was also concerned that the new Ministry of Justice may not be able to have the same sort of relationship with the lord chancellor, adding that he felt the traditional role of that job may be "watered down" because of the new responsibilities.
But Lord Falconer, who currently holds that position, insisted that there would still be proper checks and balances on the legal system after the Home Office split takes place.
"First of all there is a statutory obligation on the part of the lord chancellor, who will remain the secretary of state, to ensure there is a properly funded justice system," he told the same programme.
"There is the constitutional embedment in our constitution of the independence of the judiciary."
He added: "These are things that have been properly thought through. The issue about whether or not there should be a Ministry of Justice is something that has been in public discussion for a long time."
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