AT&T has said it will take a US$4 billion charge this quarter relating to its proposed takeover of T-Mobile USA, an apparent acknowledgement by the US operator that the proposed US$39 billion mega-deal may not now get regulatory approval to go ahead.

The firm added that it was also withdrawing the merger application lodged with the Federal Communications Commission (FCC), after the US regulator said this week it wanted to investigate the deal, potentially creating yet another regulatory hurdle.

Instead, AT&T and T-Mobile USA said they would concentrate their efforts on obtaining antitrust clearance for the transaction from the US Department of Justice (DoJ). The department is also opposed to the deal with the matter set to be heard in court early next year.

In a statement, AT&T said that it would aim to push the deal through via “the litigation pending… or alternate means” and then “seek the necessary FCC approval.”

Under the terms of the original US$39 billion merger agreement, AT&T proposed a payment of US$3 billion to T-Mobile USA-owner Deutsche Telekom “to reflect the potential break-up fees due Deutsche Telekom in the event the transaction does not receive regulatory approval.” A further US$1 billion relating to the ‘book value’ of the spectrum transfers included in the deal takes AT&T’s total liability to US$4 billion if the deal fails.

AT&T recently pushed back its intended closing date for the proposed merger by three months to the middle of 2012 due to the intense regulatory scrutiny the deal has come up against. The Financial Times this week reported that “most analysts think there is a less than 50:50 chance” that the merger will go ahead, unless significant concessions are made ahead of the court hearing in February.

In an emailed statement to Bloomberg earlier this week, AT&T senior VP of corporate communications Larry Solomon said the company is reviewing all options, adding that the FCC’s intervention is “disappointing.”

“It is yet another example of a government agency acting to prevent billions in new investment and the creation of many thousands of new jobs at a time when the US economy desperately needs both,” Solomon said.

Rivals such as Sprint Nextel have argued that the combination of two of the big four national US operators would reduce competition in the market and lead to higher prices for consumers.