Shropshire Council's northern planning committee has approved the proposal to redevelop the Pauls Moss area of the town.
It comes after members rejected the original plan earlier this year in order to retain Pauls Moss House which was at risk of being demolished.
Wrekin Housing Trust returned last month with a fresh application which proposes to retain the historic mansion and convert it into a cafe and community hub.
Further concerns were however raised regarding the lack of on-site parking.
Thomas Biggins, Shropshire Councillor for Whitchurch North, said: "I support the medical centre as I have done from the beginning, however, there is a shortage of parking. It will require 51 car parking spaces but only 36 are being provided. This quite frankly is not acceptable - it's clearly not enough.
"If you drive in through the main entrance and can't park, you will have to leave and come back in through the other entrance and it's going to cause utter chaos. I'm just trying to avoid a parking crisis."
But Councilor Vince Hunt, who sits on the planning committee, said members need to weigh up the need for a new medical centre against the parking situation.
He said: "This is a difficult one. It strikes me that whenever there is something built in urban areas that parking is a problem. Of course we would love to have more parking, wider spaces and double the amount we need, but that's not the reality in urban areas.
"I don't know how we can fix parking but I do know there was a huge amount of disappointment in Whitchurch when it was turned down last time. It's my belief that it's never going to be ideal but we have obtained the best we can and the best of both worlds. This will provide extra medical provision for the town while also retaining Pauls Moss House."
The authority's highways department raised no concern about the parking and said there is sufficient provision within walking distance.
Councillor Nick Bardsley asked for the parking situation to be addressed in the transport plan and made a suggestion that the on-site parking should be for patients only - not staff.
Wayne Gethings, group chief executive of The Wrekin Housing Group said “We are pleased that the application has been successful. The scheme includes a brand new doctor’s surgery, much needed affordable housing with onsite care provision and a vibrant community space.
"We are looking forward to starting on site soon and, along with our project partners, delivering this modern medical and care development that will make a real difference to people’s lives in Whitchurch and north Shropshire.”