The left-arm quick had been complaining of soreness in his right foot during the second Test and scans on Friday confirmed the worst, leaving Australia without its most dangerous bowler for the final two matches in the Border-Gavaskar series.

For the second time in 16 months, Starc faces a decent spell on the sidelines though there remains hope he will be available for the Champions Trophy one-day international tournament in England starting in June.

Selectors are yet to name a replacement however injury-plagued young guns Pat Cummins and James Pattinson are the favourites to get the call-up.

The news came as Cricket Australia and the Board of Control for Cricket in India called a cease fire on the angry war of words which erupted in the aftermath of a spiteful second Test.

Having proven he can be a menace on any surface, Starc's setback has the potential to be a major series changer heading into the third Test starting in Ranchi on Thursday.

Starc's express pace had been earmarked as one of Australia's most dangerous weapons in India, where reverse swing plays a major part on the abrasive wickets.

He played key roles with bat and ball in Australia's shock Test win in the first Test, and though well down by his usual standards in Bangalore he triggered a second-innings collapse which swung the game back in the visitors' favour.

Starc suffered a stress fracture in his right foot during the day-night Test of 2015 but this injury is believed to be to a different area.

The 27-year-old, who also suffered a nasty gash to his knee in a training mishap in September, has done well to play 11 consecutive Tests but it has taken its toll.

He had already withdrawn from the Indian Premier League on the eve of the Test series, turning his back on a $973,000 pay cheque.

"Mitchell experienced some pain in his right foot during the second Test in Bangalore which unfortunately had not subsided a few days after the Test as we had hoped," Australia's team physiotherapist David Beakley said.

"We made the decision to scan his foot in Bangalore this morning and unfortunately it has revealed a stress fracture.

"Subsequently, this means Mitchell will be unavailable for the remainder of the tour of India and will return home to Australia to start his rehabilitation."???

Starc's injury adds to a dramatic few days where relations between Australia and India plunged to a nine-year low in the wake of Virat Kohli's explosive allegations of systematic cheating of the decision review system.

The BCCI lodged a complaint late on Thursday with the International Cricket Council against Australian captain Steve Smith and batsman Peter Handscomb after they consulted the dressing room for assistance.

The pair had been facing a charge of breaching the spirit of cricket but the BCCI withdrew the complaint hours later after scheduled talks with CA chief James Sutherland in Mumbai.

Sutherland had been en route to the airport to fly home when he received the call from the BCCI, asking for both boards to issue a joint statement calling a truce.

The fiasco has reaffirmed the ICC's reluctance to confront India and the turmoil within the BCCI after a committee appointed by the Supreme Court recently called for a complete overhaul of the game.

CA had believed the ICC, which did not lay a charge, needed to take a stronger stance on poor player behaviour from both sides.

Sutherland had the power report Kohli for bringing the game into disrepute with his unfounded cheating allegations but it's believed he would not have done so even if the cease fire had not been called.

The BCCI had called for peace in a statement issued on Wednesday in support of Kohli only to slap charges 24 hours later before backflipping again and calling for a truce.