Laura Muir and Jemma Reekie have unexpectedly cut short their altitude training camp, leaving long-term coach Andy Young in South Africa.
UK Athletics confirmed the Scottish pair returned home last week.
The governing body say staff are working with both athletes "to ensure they receive the support they require" for training and competition.
Muir, 29, and Reekie, 25, are training partners and friends.
The pair have worked with Young throughout their careers, with Muir claiming a 1500m silver medal at the Tokyo Olympics in 2021 and a world championship bronze in the same event last year.
Muir and Reekie regularly travel with Young to South Africa for training, but the Times newspaper reported they have fallen out with their coach.
Young told BBC Scotland: "There was no bust-up. I think you would find the girls were worried about my health if you spoke to them.
"Felt I wasn't looking after myself properly, maybe thought pressure was getting to me. I'd say they were reading too much into it."
Muir and Reekie are aiming to compete at the Olympics in Paris next summer.
A UK Athletics spokesperson said: "UK Athletics can confirm that Laura Muir and Jemma Reekie left their altitude training location last week to return home to the UK.
"World Class Programme staff and services are continuing to work with both athletes to ensure they receive the support they require as they review their training and competition programmes for the season ahead."