There was outrage last month when The Evening Telegraph discovered the ban had been brought in amid fears for the safety of the men and women from the nearby airbase.
RAF Wittering station commander Group Captain Ro Atherton had taken the decision after taking advice from military police.
The RAF said personnel had been suffering repeated verbal abuse when out in the city and they were keen to prevent problems escalating.
Much of the alleged abuse centred on the force's operations in Iraq and Afghanistan.
The ban sparked a heated reaction from people across the world, and The ET was flooded with messages of support telling RAF personnel to proudly wear their uniform in public.
Grp Capt Atherton called a meeting with city Mayor Cllr Marion Todd and Cambridgeshire police Chief Superintendent Paul Phillipson, and a decision was made to uphold the ban.
Now Mr Jackson has written to the Minister of State (Armed Forces), Bob Ainsworth expressing his disapproval.
In response, Mr Ainsworth said: "I would like to assure you that the decision to restrict the wearing of uniform by service personnel in Peterborough was not undertaken lightly. Personnel stationed at RAF Wittering have traditionally had an excellent relationship with the people of Peterborough and, with the exception of only a small section of the local community, continue to do so.
"Wherever possible and appropriate we encourage armed forces personnel to wear their uniforms with pride. However, the safety of our personnel must always be a priority."
He added: "As the local station commander, Group Captain Atherton was best placed to make such a decision concerning local security matters. With the best interests of RAF Wittering personnel in mind, the decision was made, with regret, with the intention of reducing the likelihood of further service personnel, who live and work in the Peterborough area, being identified and targeted by criminals or others.
"The instruction restricting the wearing of uniform in Peterborough continues to be kept under review with both Cambridgeshire police and Peterborough City Council."
Mr Jackson, who has compared the CO's decision to "using a sledgehammer to crack a nut" in the past, said: "It is very unsatisfactory that a decision taken by the base commander on the basis of an incident 18 months ago should have caused Peterborough's reputation to be so badly damaged in the national and international press.
"I think she should reconsider it. The city has suffered as a result of it."
Special report: RAF uniform row, March 2008.
The full article contains 439 words and appears in Peterborough ET newspaper.