Cooper left a position with Boro's youth team in May to take charge at League Two outfit Hartlepool United.
The former England international is taking the managerial reins for the first time and is hoping to put his connections in the game to good use as he cuts his coaching teeth.
It has been suggested that he will return to Middlesbrough in an effort to land a number of the club's promising youngsters on loan.
Mowbray sees no reason why agreements cannot be reached, as long as the deals are beneficial to all concerned.
He told the Gazette: "We will try and help Coops as much as we can.
"He has asked me for some players and my first priority is to look after our club and make sure we're strong enough with numbers.
"But there will come a time where some of the younger players are not making the 18 and if we feel as if it's right to go and help Coops and Hartlepool, then we'll allow them to do that.
"Obviously there are a few parties that need to agree that of course, but if can help them along the way we'll try."