Strauss suggested the issues surrounding Pietersen "will take a while to be resolved", adding "we'll be looking to do that away from the public eye as much as possible in the coming weeks".
England coach Flower told BBC Sport: "When we have time we will begin resolving these issues one way or another. This is not just an issue between the player and the captain, there are bigger issues at heart.
"The text issues have to be investigated so that we know what situation we are dealing with. We are aware of some of the content but we have to understand the content to move on in a proper, healthy fashion."
Asked if a decision had been made on whether to offer Pietersen a new central contract, Flower added: "We have to deal with some of these other issues before a decision can be made on central contracts and who gets offered them."
England Twenty20 captain Stuart Broad has been left out of the one-day series against South Africa to rest ahead of the World Twenty20.
England play five one-day internationals against the Proteas - the first on 24 August in Cardiff - and three Twenty20s before they commence the defence of their World Twenty20 crown in Sri Lanka.
"Stuart Broad has an important period coming up leading our T20 side and with a three-match series followed closely by the ICC World T20 we feel a two-week break from cricket is in the best interests of both Stuart and the team," national selector Geoff Miller said.
England NatWest ODI Series squad:
Alastair Cook (Essex) (captain), James Anderson (Lancashire), Jonny Bairstow (Yorkshire), Ian Bell (Warwickshire), Ravi Bopara (Essex), Tim Bresnan (Yorkshire), Jade Dernbach (Surrey), Steven Finn (Middlesex), Craig Kieswetter (Somerset), Eoin Morgan (Middlesex), Samit Patel (Nottinghamshire), Graeme Swann (Nottinghamshire), Jonathan Trott (Warwickshire), Chris Woakes (Warwickshire).
England squad for ICC World T20:
Stuart Broad (Nottinghamshire) (captain), Jonny Bairstow (Yorkshire), Ravi Bopara (Essex), Tim Bresnan (Yorkshire), Danny Briggs (Hampshire), Jos Buttler (Somerset), Jade Dernbach (Surrey), Steven Finn (Middlesex), Alex Hales (Nottinghamshire), Craig Kieswetter (Somerset), Michael Lumb, Nottinghamshire), Eoin Morgan (Middlesex), Samit Patel (Nottinghamshire), Graeme Swann (Nottinghamshire), Luke Wright (Sussex).
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