About 500 workers were told by Laing O'Rourke earlier this week that they could leave the site on Thursday, avoiding the congestion caused by thousands of visitors coming to the airport to watch the landing.
However, the firm then changed its mind after it became concerned that workers might want to re-enter the site on Friday to watch the landing – which would make it difficult to control access.
A project insider said: "Laing O'Rourke want to guard against any large-scale movement of the workforce."
The issue was raised on Wednesday at a meeting of construction unions and Laing O'Rourke. A BAA spokesperson said: "Due to the congestion expected on the site on Friday, workers are being offered the opportunity to leave the site at 1pm. This was agreed some time ago and we are not aware that some workers were offered the chance to leave the site on the Thursday."
Laing O'Rourke were unavailable for comment as Building went to press.
The issues of bonus payments and working hours were also addressed at the Wednesday meeting. As Building revealed last week, workers are unhappy that they have to clock on at the site 20 minutes early in order to have time to reach their places of work.
GMB national construction secretary Phil Davies said he was now writing to Laing O'Rourke so that the issue of working hours at T5 could be referred to the union's national leadership.
He said: "Our feeling is that this is the kind of issue that could easily turn into a full-scale dispute as the workers are very concerned about it." He said that he hoped the issue could be resolved quickly and fairly.
Davies added that there had not been any real change on question of bonus payments. He said: "This problem could well be an administrative error."
BAA said that all the terms and conditions had been agreed by Laing O'Rourke and the unions in an all-encompassing pay agreement. He would not be drawn on this specific dispute.
In July, Building revealed that Laing O'Rourke and the construction unions were locked in talks over a dispute on the bonus payments that workers were receiving on the site.
Workers had threatened a strike ballot over the issue after it emerged that some sections of the site were receiving a greater amount of bonus payments than others.
Union leaders and Laing O'Rourke officials met in a London hotel and decided that the bonuses would be reviewed every three months.