Anderson looked fit on his return to the team in their 216-run hammering of a local side in Canberra on Monday, but sat out Wednesday's win over the Prime Minister's XI.
Morgan said the decision was made to rest their spearhead to give him the best possible chance to play in Friday's tri-series opener.
“It was more managing his workload coming back from injury,” Morgan told reporters. “We decided that he wouldn't be able to play three games in a week. So in order for him to be fit for selection, we needed to up his workload in the nets.”
Anderson is the only injury concern heading into the one-day international. "Everybody else is, to my knowledge, at the moment fit for selection," added Morgan.
The skipper praised Ian Bell's 187-run knock against the Prime Minister's XI, the highest innings by an England batsman in a competitive 50-over match, and said it epitomised the ruthlessness his side needed to succeed.
Their first priority will be to beat India and Australia in the tri-series to boost confidence ahead of next month's World Cup.
"It'll be nice to be sitting here at the end of this series with some silverware and be confident in where we're going as a side," he said. “I know throughout this series it might throw up a couple of things because Australia can be a difficult place to tour, a difficult place to adapt to conditions, but I certainly think that we're one of the sides that finds it a lot easier to adapt.”
Dhoni refuses to elaborate on retirement decision
Ahead of leading India in the ODI tri-series against Australia and England, MS Dhoni refused to elaborate on his sudden retirement from Test cricket.
The 33-year-old stunned the cricketing world — and a completely unaware India team — when he announced his immediate Test retirement after the drawn third Test against Australia in Melbourne last month.
India's World Cup-winning captain again had nothing to say in the subject as he launched the Indian one-day team's new kit ahead of their first tri-series game against Australia in Melbourne on Sunday.
The closest he came to addressing the issue was when he was asked about his time off since that Test. “”It has been good, a few days off," he said.
And that was it. There were a few prepared comments about the uniform, but no questions were allowed from the assembled journalists.
The microphone was handed to Kohli, one of the few Indian players to enhance his reputation during the 2-0 Test series loss to Australia.
"It's been a very eventful month and a half since we came to Adelaide," said Kohli. “I've enjoyed every day of it. It's been challenging at times, but that's where international cricket is.
Dhoni, who is one of the world's highest-earning sportsmen, was India's most successful Test captain, winning 27 of the 60 Tests he led the national side in, with 18 losses and 15 draws.
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