But Gill insisted the figure is still "pretty good" in the current economic climate and that the club is in good financial shape.
Gill said the number of season tickets sold was 51,800 compared to the target of 54,000, and that executive seat sales were "on track".
United's season ticket sales have been conducted against a backdrop of a campaign by fans' group the Manchester United Supporters' Trust (MUST) urging a boycott in the hope of persuading the American owners, the Glazer family, to sell the club.
Asked about the season-ticket protest, Gill said: "I'll be clear on that. Last year our target was 54,000 season tickets, we've sold 51,800, which is pretty good in the current climate.
"We've sold more season tickets than the capacity of most Premier League grounds. Our executive seat sales are on track as compared with last year in a different market.
"I think the bare facts are that the club is in good financial shape. The ticket sales have held up. We sold out for Newcastle and West Ham but we are not complacent and we've got to keep working to make sure that we fill the ground for every game and we'll do that by playing great football, attractive football, exciting football that brings fans in."
The protest against United's owners surrounds the debts they took on to buy the club. These now stand at more than £700million - including a £500million bond scheme, and £202million in payment in kind (PIK) loans.
BBC's Panorama claimed earlier this summer the Glazers' shopping mall empire in America was facing problems but Gill would not be drawn on that, stating instead the club was very successful financially and were comfortable with the position.
Gill added: "I'm not going to comment on that [Panorama]. We've had another very successful year off the pitch when we announced our results for June 2010 they were excellent, generating cash.
"We have put in place a long-term financial structure for the club with the bond, obviously that's serviced on a regular basis.
"So no I don't think it impacts us at all. So I think we've got to be comfortable."