The 29-year-old opening batsman has faced a barrage of criticism over his captaincy and form but will captain the team in a seven-match ODI series in Sri Lanka starting in November ahead of the World Cup which begins in February.
“We feel he is our best man to lead the team into the World Cup. He’s our number one batsman, he’s showed that in the past and he’ll show it again in the future,” Whitaker told the BBC.
“He’s our exceptional leader, he has shown huge amounts of fortitude and resilience over the summer, and I’d like to make it perfectly clear we are 100 per cent behind Alastair Cook as captain.”
Cook will lead a 16-man squad that shows little change to the one comprehensively beaten 3-1 by India, the world’s best ranked one-day team, this month.
In-form James Taylor and Ravi Bopara, who did not feature against India, were recalled and batsman Gary Ballance was left out.
“Congratulations to James Taylor who has been rewarded for his outstanding form for Nottinghamshire this season and fully deserves another opportunity in the international arena,” Whitaker said in a statement.
“While Gary Ballance will I’m sure be disappointed to miss out on this tour he knows he remains a very important part of our plans.”
Jonathan Trott, the former bedrock of England’s batting line-up, was not selected despite stating his eagerness to resume his international career.
The 33-year-old has not played for England since departing the disastrous Ashes tour in November due to a stress-related illness but recently helped Warwickshire reach the final of the domestic One-Day Cup.
“We’ve been talking about Jonathan Trott for the last few weeks and we’re very pleased he’s come back and done well for Warwickshire,” Whitaker added to the BBC.
“I’m sure throughout the winter we’ll continue to have those discussions about Jonathan because he’s been an exceptional player in the past.”
England squad: Alastair Cook (Essex) (captain), Moeen Ali (Worcestershire), James Anderson (Lancashire), Ian Bell (Warwickshire), Ravi Bopara (Essex), Jos Buttler (Lancashire), Steven Finn (Middlesex), Harry Gurney (Nottinghamshire), Alex Hales (Nottinghamshire), Chris Jordan (Sussex), Eoin Morgan (Middlesex), Joe Root (Yorkshire), Ben Stokes (Durham), James Taylor (Nottinghamshire), James Tredwell (Kent), Chris Woakes (Warwickshire) – Reuters.