But, in his extended absence, Connacht have moved to the top of the GUINNESS PRO12 table and are in the driving seat to secure European Rugby Champions Cup qualification next term.
And with Cooney now having committed himself to Connacht for a further 12 months, Lam is excited for what the future could hold at the Sportsground.
"If we are going to be playing Champions Cup rugby next season it is vital we have quality depth and competition in key positions such as scrum-half," Lam said.
"I'm really pleased that John has committed to not only compete but also continue to grow his game with us at Connacht Rugby.
"John is an extremely hard-working individual and we have a lot of belief in his ability so we're delighted that he has signed on for another season."
Cooney has not featured for Connacht since November following shoulder surgery.
But the 25-year-old believes he is closing in on a first-team return.
"I am determined to push for a place in the team for what will be some really tough games and an exciting finish to the season," Cooney said.
"Although it's been a frustrating few months with my injury, I'm really happy to have my future secured with Connacht for next season.
"I was really enjoying my rugby at the start of the season and I'm looking forward to pushing on now following my rehab."
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