Announcing the decision, Director of Public Prosecutions Keir Starmer said prosecutors had decided there was sufficient evidence and it was "in the public interest to charge the individuals concerned".
But in a joint statement, the three MPs said they were "clearly extremely disappointed" that charges were being brought.
"We totally refute any charges that we have committed an offence and we will defend our position robustly," the statement said.
"We are confident of our position and have been advised by eminent QCs."
They added that the issue should have been resolved by the Parliamentary Commissioner for standards and said while the expenses system had been "utterly discredited" they believed there had been "a complete inconsistency of approach to different individual cases".
Former minister Elliot Morley, MP for Scunthorpe, faces charges relating to a total of £30,000 of mortgage claims which, it is alleged, were "in excess of that to which he was entitled" and covered a period when there was no mortgage on the property.
CPS CHARGES LAID
Elliot Morley - two charges over £30,000 of mortgage interest claims
David Chaytor - accused of dishonestly claiming £1,950 for IT services and also £18,000 in rent
Jim Devine - accused of claiming £3,240 for cleaning services and £5,505 for stationery
Lord Hanningfield - faces six charges of dishonestly submitting expense claims
David Chaytor, MP for Bury North, is accused of "dishonestly claiming" £1,950 for IT services and further sums of £12, 925 and £5,425 relating to rent on properties which he and his mother allegedly owned.
Livingston MP Jim Devine is accused of "dishonestly claiming" money for cleaning services and for stationery using false invoices.
Speaking outside his home he said it was the charges that were being brought were new and could be easily explained, adding: "I'm absolutely distraught and astonished at the decision that's been taken today."
Paul White - the Conservative peer Lord Hanningfield and leader of Essex County Council - is accused of dishonestly submitting claims "for expenses to which he knew he was not entitled" - including overnight stays in London.
He stepped down as council leader on Friday and as a Tory frontbench spokesman.
He denies the charges and says he will "vigorously" defend himself against them adding: "All the claims I have ever made were made in good faith. I have never claimed more in expenses than I have spent in the course of my duties.
"To avoid any embarrassment or distraction for my party, I am standing down from my frontbench duties in the House of Lords with immediate effect."
Jim Devine denies charges of falsely claiming expenses
The Conservatives said Mr Cameron had also asked the party's leader in the Lords, Lord Strathclyde to suspend the Conservative whip from Lord Hanningfield.
David Chaytor and Elliot Morley were suspended from the parliamentary Labour party last May.
The expenses saga continues to rock Westminster - on Thursday 372 MPs were ordered to repay money totalling £1.1m, claimed in second homes expenses over four years.
Prime Minister Gordon Brown said he was "very angry about what has happened" as he arrived in Exeter for a regional Cabinet meeting.
He said: "We took steps some months ago to remove the right of these people to stand as candidates for the Labour Party. These are very serious criminal allegations. All criminal allegations have got to be investigated. It's a matter now for the courts."
The solicitors acting for Labour peer Lord Clarke said he was "hugely relieved that the nine month investigation into his claims under the House of Lords' Allowances Scheme has ended at last, and that he has been cleared of having committed any criminal offence".
CPS statement on MPs' expenses
Legal analyst Joshua Rozenberg told the BBC that Keir Starmer and the MPs' joint statement implied that the issue of Parliamentary privilege might be used by defence lawyers.
It traditionally guarantees MPs and peers immunity from slander laws for statements in Parliamentary debate and also relates to access to the Parliamentary buildings.
But he said it appeared that lawyers had suggested it may extend to the charges faced - the MPs' statement said it was "an issue that should be resolved by the parliamentary commissioner who is there to enforce any breach of the rules".
In his statement Mr Starmer said: "We have considered that question and concluded that the applicability and extent of any Parliamentary privilege claimed should be tested in court."
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