Kevin Pietersen has been left out of the England squads for both the World Twenty20 and the preceding one-day series against South Africa.
The 32-year-old was dropped for the third Test against South Africa after allegedly insulting Test captain Andrew Strauss in texts to the tourists.
Pietersen apologised for the messages, admitting they were "provocative".
England team director Andy Flower said: "There's unresolved issues of trust and respect which have to be resolved."
Pietersen had been expected to meet Strauss this week to discuss the matter but speaking after his side's defeat by South Africa in the third Test on Monday, the England captain said that as far as he was concerned that would not be the case.
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.
Pietersen retired from both one-day and Twenty20 internationals in May, but made himself available for all formats in a surprise U-turn on 11 August.
Despite being man of the match in the second Test against South Africa the off-field controversy led to him being dropped for the third Test, and he was on Sunday.
The big-hitting right-hander averages 41.84 in one-day internationals with a strike rate of 86.76, while in T20s he averages 37.93 with a strike rate of 141.51.
He was named player of the tournament as England won the last World Twenty20 in 2010, averaging 62 from his six innings.
Luke Wright and Michael Lumb, who were both part of the side that won the World Twenty20 in 2010, return to the T20 squad for the first time since June 2011.
Also in the 15-man T20 squad is Danny Briggs, who has a solitary ODI cap for England but has yet to represent his country in the shortest form of the game.
Ravi Bopara, who has not played for England since pulling out of the squad for the second Test against South Africa for personal reasons, is included in the ODI and T20 parties.
The Essex all-rounder will play for Gloucestershire in the one-day tour game against South Africa at Bristol on Wednesday.
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).