Tim Paine led Australia in the final test of the South Africa tour after Steve Smith was dropped over the ball tampering scandal.

Australia may be down to their third choice captain when they take on England in a one day international series in June.

Injured captain Tim Paine is set to resume full training within weeks, but is no guarantee to lead the side through the ODI series. Paine himself has the top job after Steve Smith was banned from top level cricket following the ball tampering scandal.

Paine suffered a hairline fracture of his right thumb while standing up to the stumps to fast bowler Chadd Sayers on the third day of the fourth test against South Africa at the Wanderers in Johannesburg.

GETTY IMAGES Steve Smith isn't allowed to hold a leadership position in the Australia cricket team for two years.

Scans confirmed Paine had hurt the thumb, but he at least escaped surgery, which could have ruled him out of the one-day series.

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Paine knows all about hand surgery, having had seven operations on his index finger over seven years which almost led to his retirement.

Cricket Australia said on Monday Paine would resume batting and wicketkeeping within three weeks, with the ODI squad expected to be released early next month.

That tour begins with a practice match against Sussex on June 1. The tourists will then feature in five one-day internationals, the first at The Oval in London on June 13.

Fast bowler Mitchell Starc remains in doubt for the tour, as he is still on the mend from a tibial bone stress reaction in his right leg which ruled out of the fourth test against the Proteas and the Indian Premier League. Medical staff will review him again in a few weeks.

While Paine is likely to be fit for the tour, it remains to be seen if he will captain the side, for he has only been confirmed as test captain. Cricket Australia would only say an ODI skipper will be named when the squad is released.

There is much for team performance boss Pat Howard and the selectors to debate, for Australia has major series and tournaments in the sport's three formats in the next 18 months.

Paine, 33, has already shown his aptitude for the top role in the test team, and is seen as having the right character to help usher in a new culture that will flow from a review conducted by former test batsman, Rick McCosker, in wake of the heated series in South Africa which led to the suspensions of Steve Smith, David Warner and Cameron Bancroft.

However, the selectors may not want to overburden him, and could return to the days when there were separate test and ODI captains.

Warner led the Australian Twenty20 side to a tri-series victory in New Zealand in February but is suspended and will not be considered for a leadership role in the future.

Victorian Aaron Finch, who led the T20 side between 2014 and 2016 and has deputised in one-day internationals, would be in the mix for the top job in the white-ball formats, with the World Cup in England next year the major lure. State captains Mitch Marsh, who has had ankle surgery, and Travis Head would also be in the mix.

CA has yet to begin a formal search for a new coach to replace Darren Lehmann. That role could also be split between red-ball and white-ball cricket. Justin Langer remains the favourite for the Test position, Jason Gillespie will also be in the mix while Ricky Ponting, in charge of the Delhi Daredevils in the IPL, has been touted as a short-form national coach.