Eoin Morgan believes Jofra Archer's three-month injury lay-off may be a blessing in disguise, allowing the paceman to reset himself after a difficult first winter on England duty.

Archer struggled with the Kookaburra ball on the flat pitches of New Zealand – where he was racially abused by a spectator at Mount Maunganui – before an elbow complaint led to him missing the final three Tests in South Africa.

Once it was discovered he would miss the Twenty20 series he returned to the UK, where a scan earlier this week detected a low grade stress fracture of his right elbow, which will sideline the 24-year-old for an extended spell.

The problem first surfaced last summer when Archer lit up the World Cup by being England's leading wicket-taker in the triumphant campaign, following that up with a starring role in the Ashes.

While this enforced absence is far from ideal, Morgan, England's limited-overs captain, believes it has its advantages and dismissed suggestions the injury will be a lingering issue heading into this summer.

"I don't think so. He carried some niggles throughout the summer, one was through the World Cup, definitely, and it was managed really well," Morgan said.

"Jofra hasn't had a serious injury for some time now and I don't think this is a major issue.

"It allows him time – particularly when it's in his elbow – both to spend some time at home and get away from the game but also recondition exactly what he's built to do.

"We play a lot of cricket and stepping back from it sometimes, you reap the rewards and the benefits later down the line."

Archer will miss next month's two-Test tour of Sri Lanka as well as the Indian Premier League, with a view to returning for the first of three Tests against the West Indies in June.

As a fast bowler capable of exceeding 90mph regularly, there has been some suggestion that his workload should be managed carefully, but Morgan thinks that is already being done.

"They already are, he missed the T20 tour to New Zealand," Morgan responded.

"Everybody who plays all three formats is always an area where we need to manage both their gametime and time away from home."

Archer would have been rested from the ongoing one-day international series against the Proteas had injury not intervened, with Ben Stokes, Jos Buttler and Mark Wood also sitting out.

Fellow World Cup winners Moeen Ali and Adil Rashid are part of the squad but were unused in the defeat at Cape Town on Tuesday and the Durban washout on Friday, when only 11.2 overs were possible because of intermittent downpours.

That leaves South Africa 1-0 ahead going into the final match at Johannesburg, where an England side low on experience need to win to a avoid a first ODI bilateral series defeat in three years.

However, how they fare in this series takes a backseat for Morgan, who is prioritising expanding their talent pool.

Morgan added: "It's not about immediate results, it's about investing time in those guys."