Shadow communities secretary Hilary Benn said Mr Pickles had broken a promise to his own constituents, who would now see council tax in Brentwood soaring for some by as much as 20%.
Eric Pickles has been "masterminding a council tax increase for those who can least afford it" while travelling the country lecturing councils to freeze the bills, Labour has said.
The Government is handing control of council tax benefit to local authorities and allowing them to determine how the money is allocated among claimants.
Speaking during a questions session in the Commons, Mr Benn said: "Why is it, because councils up and down the country, Tory and Labour, have been put in an impossible position.
"Isn't it the truth that the very lowest paid are going to be in a very difficult place? Not my words but those of the Conservative leader of the Local Government Association.
"The Secretary of State has been travelling up and down the country lecturing councils about not increasing the council tax, all along he has been masterminding a council tax increase for those who can least afford it.
"Don't you understand the public will see this happening in the very same month the top rate of tax is cut and say this is unfair?"
But local government minister Brandon Lewis insisted: "I'm afraid you oversimplify things.
"What you haven't touched on is local authorities, as we have said, have got the right to look at their local communities, design schemes they think are right for their communities, not a central diktat like the last Government used to do.
"The authority you have mentioned in Brentwood is a good example because what you haven't mentioned is the way they have changed the taper to make sure it does pay to work."