A statement on Team Sky's website said Henao had not failed an anti-doping test but had been contacted by world governing body, the UCI, and Cycling Anti-Doping Foundation (CADF) with regards to his Athlete Biological Passport (ABP) data between August 2011 and June 2015.
"It is our hope that this can be looked at and resolved quickly by all the relevant authorities so Sergio can start racing again soon," a statement said.
Henao, 28, a specialist climber signed with Team Sky in 2012 and finished in the top-10 in his first Grand Tour, the 2012 Giro d'Italia.
He was voluntarily withdrawn by the team for three months in March 2014 after their own monitoring of his ABP and his out-of-competition tests during his usual winter training block back home at high altitude in Colombia.
Sky commissioned an independent 10-week research programme into the biological characteristics of riders who live and train at high altitude with the results revealing nothing to raise suspicions of any wrongdoing by Henao.
He returned to racing but suffered a serious crash at the Tour de Suisse in June, 2014, fracturing his patella.
The latest probe into his ABP by cycling anti-doping authorities is another setback although Sky's Team Principal Dave Brailsford said he fully supported his rider.
Henao said he was confident the issue would be resolved soon but added: "I am beyond disappointed. I have worked incredibly hard to get back to racing fitness after shattering my knee, but I know who I am, how hard I have worked and the sacrifices I have made to be where I am today."
Team Sky say they stand by the conclusions of the independent research carried out in Sheffield and said that they had been under no obligation to withdraw Henao.
"This is team policy if and when a formal process such as this begins," the statement said.
Brailsford said the issue of 'altitude natives' remained a complex area and that the science was still limited.
"We have proactively sought to understand it better by undertaking detailed scientific research -- both for Sergio and for the benefit of clean sport more widely," he said.
"Thus far, Sergio's data has been anonymous to the CADF experts. We hope and believe they will reach the same conclusions when they consider the background and all the evidence over the coming weeks."