The problems led Laing to bring in US troubleshooter Bechtel to complete the project in July.
An NAO spokesperson said it had started work on the investigation. However, he added that nothing would be published "until the dust settles on the matter". Laing refused to comment on the probe.
The news follows the completion of the sale of Laing's construction arm to concrete subcontractor O'Rourke for £1, nearly a year after the group put the £700m subsidiary up for sale.
New owner Ray O'Rourke said he intended to revitalise the construction division, combining it with O'Rourke operations to create a £2bn group in three to five years.