The Federal Opposition says the resignation of the head of construction for the $36 billion National Broadband Network (NBN) is very concerning.

Patrick Flannigan resigned earlier this week after 14 months with NBN Co.

It came after NBN Co broke off its five month tendering process with construction firms, arguing the companies' quotes were overpriced.

Opposition Communications spokesman, Malcolm Turnbull, says secrecy and uncertainty around Mr Flannigan's departure is troubling.

"If this was a listed company you can only imagine the direction its share price would be going," he said.

"This is one of the problems with the NBN - it is so unaccountable.

"The Government has done everything it can to prevent scrutiny of the NBN."

Mr Turnbull says it is clear the Government cannot deliver the project on budget by 2020.

"That shows that their estimate of what it was going to cost to get this work done was too low, so we don't have confidence in their budget," he said.

"The head of construction has left - no explanation given, no interviews given, no accountability given - this is a $50 billion project."

Mr Flannigan managed the construction of the NBN's first release sites in Tasmania.