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Jos Buttler, the team's vice-captain, will take charge in Morgan's absence, with squads for the three ODIs and two Tests set to be announced on Friday. Morgan and Hales were foremost among the players to have spoken of their uncertainty about going to Bangladesh, after a terrorist attack in July, and communicated their intentions to Andrew Strauss, England's director of cricket, at the weekend.
Did Morgan and Hales make the right decision by pulling out of the Bangladesh tour?4 votes
Yes - Safety is a personal choice and must be respected
No - The ECB deemed the tour safe so they should have gone
"Whilst we understand and respect Eoin and Alex's decision, we are disappointed that they have made themselves unavailable for selection for the Bangladesh tour," Strauss said. "We have had open and honest conversations with all the players about the security arrangements in Bangladesh and at this stage we are not expecting any other individuals to withdraw from the tour. Final selection for the Bangladesh tour, will now take place on Friday.
"As with all England overseas tours, the safety and security of players and staff is of the utmost importance to ECB. We will continue to monitor the situation in Bangladesh, take advice and consider the appropriate steps up to and throughout the five weeks we are on tour."
Morgan was reported to have told Strauss he would not be going to Bangladesh before the players went for their end-of-season assessments at Loughborough on Friday and Saturday. Those in line for selection were given until this weekend to make a final decision on whether they would accept the recommendation of the ECB's security advisor, Reg Dickason, that the tour should go ahead as planned.
Strauss has said he believes it is "100% safe" to tour, after a delegation including Dickason, the PCA chief executive, David Leatherdale, and ECB director of cricket operations, John Carr, reported back last month.
In a statement on Sunday, the ECB said: "A thorough and detailed risk assessment was approved and accepted by the ECB board and the England players and management have been fully briefed on all aspects of the safety and security arrangements."
Earlier in the week, Morgan gave details about previous security scares he had experienced on the subcontinent. He referred to a bomb going off in Bangalore while he was playing at the IPL in 2010, as well as political unrest in Bangladesh in 2013. Last year, Australia cancelled a tour of Bangladesh on government advice and did not send a team to the Under-19 World Cup.
"I have been to places before when things have become a distraction and once or twice when that has been security, and when it has been I told myself I would not put myself in that situation again," Morgan said. "Playing international cricket - or any cricket - is not about worrying about different things, it should be the best time of your life, it should be something that you are looking forward to and wanting to do well in and are able to focus on."
While the ECB made clear that the decision whether to tour would be down individuals and no player would be penalised for pulling out, Strauss had been hopeful that Morgan would join Alastair Cook, the Test captain, in committing himself to the tour.
"Would I like both our captains to be on that tour? Absolutely, definitely," Strauss said on Wednesday. "The captain has certain roles and responsibilities that are greater than just looking after themselves. He obviously has a duty to the team. But they're still human beings - and I think that's an important point to make. They have their own thoughts, concerns, issues and views on life - and we've got to understand that."
With Buttler taking charge for the ODIs in Bangladesh, England may have to make a decision about the captaincy in the longer term, ahead of limited-overs series in India and West Indies scheduled for the start of 2017, followed by the Champions Trophy. Morgan has overseen great success since the 2015 World Cup, with England winning four of their last six ODI series, as well as reaching the final of the 2016 World T20.
For Hales, the decision could have immediate ramifications for his international career. While he is a regular in the limited-overs teams, his Test place is far less secure after failing to record a century in 11 matches; opting out of the two Tests against Bangladesh is likely to see Hales omitted for the subsequent India series as well, with Lancashire's 19-year-old opener Haseeb Hameed tipped to replace him, although he may have been dropped in any event.