Creme Developments originally wanted to build a six-storey block of 49 flats and a shop on a former petrol station site at the junction of Great Western Road and Montague Street.
The city council planning committee threw it out in April 2010 on the grounds that it would be an overdevelopment and the decision was upheld by the Scottish Government.
A second attempt to build 45 flats on the Woodlands Conservation area was also rejected the following March.
The developers were finally given the green light to construct 45 flats and two retail units in June 2011 and they have now begun building.
But last Tuesday council bosses voted to allow plans to increase the development by four homes, to 49 flats.
The move has sent shock waves through the community.
West End resident and chairman of Woodside Community Council Steve Bailey called it, "manifestly unjust and unfair".
He said: "When it was announced at our community council meeting, there was a sharp intake of breath.
"Local people can't believe it. They are shocked and totally mystified by this turn around and the strange turn of events. It makes a mockery of the whole DRS (Development Regeneration Services) system.
"The developers eventually got permission and people could live with it but they've gone and put this application in when no one's looking.
"It's like everyone has thought: 'To hell with local people'."
The extra homes are to be slotted into a new rooftop penthouse space.
The committee also voted to allow eight off street parking spaces.
The rest of the £4.2million scheme, which is being designed by Elder and Cannon Architects, is to be built over five floors.
Tom Johnstone, former secretary of Woodlands and Park Community Council, called for an overview of the whole planning system.
He said: "The planning system in Scotland is quite simply not working in a way which allows any meaningful input from ordinary members of the public.
"It is sneaky because an extra four flats isn't viewed with as much importance as the whole development."
Councillor Nina Baker, a member of the planning committee who moved to refuse the application, said it was "disgraceful".
She said: "I was very surprised that it went through.
"It basically implies what we have long suspected – if developers keep at it for long enough they will always get what they want.
"I thought it was disgraceful and I feel for the people who live around the site."
The site has been vacant since 2004 after a petrol station dating back to the 1970s was demolished.