The developer, Aire Regeneration, and regeneration agency English Partnerships had intended to sign a development agreement in March this year. This is has now been put back to June.
An investigation on the site was undertaken by Skanska in 1999. It later became apparent that further investigation was needed before planning permission could be granted, and to obtain National House Building Council warranties for the scheme.
So in April this year, Aire Regeneration asked Skanska to make a second survey to ensure that the site was safe to build on. This included the identification of the precise location of a mineshaft.
A spokesperson for English Partnerships said, now that Aire Regeneration had completed the detailed layout of the houses, it needed to "pinpoint where everything was" on the site.
He said: "We have to pinpoint the location of this mineshaft. It may be a question of designing the layout around it: it could mean repositioning one or two houses."
A source at Leeds council said the second survey was being undertaken to "validate the previous works".
She said: "[The first] set of work was for English Partnerships. The developers wanted its own assurances."
A second source close to the project said the development partners would be required to submit a detailed ground investigation report and remediation plan before detailed planning permission was granted.
He said: "They will need to prove that remediation has been done satisfactorily."
Aire Regeneration, a joint venture between housebuilders Miller and Gleeson, hopes to sign a planning gain agreement with Leeds council in June.
It aims to obtain detailed planning consent for the first 35 units in July and to start on site in the same month. The scheme was originally due to have gone on site in March last year.
Allerton Bywater timelineMay 1999M
Aire Regeneration wins second Millennium Village competition
Mentoring group set up to police design of the village.
Residents launch campaign to oppose millennium village
Allerton Bywater residents back millennium village in ballot
Detailed application for first phase of 35 houses