Gerry Gormal, the city's executive director of Development and Regeneration Services until he left in March, had reservations about a supermarket application on land owned by recently knighted tycoon Sir Willie Haughey.
If approved, the deal could reap the businessman huge dividends.
The centrepiece of the ambitious plan, lodged last year by Tesco and Cathcart Developments Ltd (CDL) , is a new superstore on 24 acres in the Gorbals, next to the headquarters of Haughey's City Refrigeration empire. The application also includes residential units, office and business space, and a new petrol station
Haughey, who is close to senior figures in the Labour Party in Glasgow, has a clear financial interest in the scheme.
In 2007, Crown Street Developments, of which he is sole director and majority shareholder, bought the land for nearly £13 million.
However, one of Gormal's final actions before he retired was to write to CDL about its plans on Haughey's land.
In his letter, dated February, Gormal said he believed the scheme could be contrary to some of the council's policies.
He said the site was designated for industry and business, but claimed parts of the proposal "would represent a significant loss of the industry and business opportunity represented by this site".
The location of the new development, Gormal said, was a "significant barrier which is likely to limit pedestrian access by the key community that the store is intended to serve".
He also said there was "little prospect that the proposal ...would generate linked trips with any town centres and, therefore, little prospect the store would contribute to town centre vitality or viability".
Another potential issue is that an application for a supermarket has been lodged for a nearby site, but this separate proposal is in the middle of a residential area.
The fate of the two applications will now be determined by the council's Labour-dominated planning committee, which could overrule objections and approve an application that would transform Haughey's derelict site.
If it passes, CDL has an option to buy all his land, which could make him millions.
Haughey, whose knighthood was announced yesterday, is a self-made man who made his millions servicing fridges. He has also given generously to good causes, such as donating £250,000 to a charity launched by Glasgow's Lord Provost.
David Meikle, Glasgow's sole Tory councillor, said: "This letter reveals the extent of the former executive director's concern about a controversial application. I respected the competence and vigour with which Gerry Gormal carried out his responsibilities. I also anticipate and expect that the new director will pursue the same concerns that Gerry had with the applicant."
Graeme Hendry, SNP group leader on the council, said: "With so many new councillors on the planning committee, it is important they understand that all decisions must be made on the merits of the application in front of them and other factors must be left outside the room when deciding to grant approval or not."
Haughey said he "definitely" wanted the application approved as it would mean "400 jobs for the Gorbals". He said: "It would be a big, big disappointment if they don't get the planning approval, given all the benefit to the Gorbals."
He added: "If I was round the council, I'd be wanting to know how things were actually getting said no to at the moment, in the climate we live in, rather than yes."
A spokesman for CDL said: "Cathcart Developments and Tesco have responded in writing to the letter from Gerry Gormal."