But chief executive Andy Cullen stressed their chase of George Hirst and Hayden Carter doesn’t rest solely in their hands.
The clamour to land the pair has intensified through impressive loan spells over the second half of the season.
Leicester City’s Hirst finished the season with 15 goals, after not bagging his first finish until November in his 14th game.
Meanwhile, Carter was a revelation after arriving from Blackburn in January, with his performances in the middle of defence and down the right flank going down a storm with Pompey fans.
Speaking after last weekend’s final-day 4-1 loss at Sheffield Wednesday, Cowley said he’d identified the pair as players he’d like to keep and it was now up to the club to ensure they return next term.
Carter has since spoken of his desire to play Championship football next season, although he is open to the possibility of a Pompey return.
Hirst, meanwhile, has indicated he would like to return but his future has yet to be decided.
Cullen stated there is the desire to land the pair, but there’s the motivations of the player and parent club to consider.
And any deals have to be on terms which work for Pompey’s summer rebuilding plans.
He said: ‘Danny would like to keep them (Hirst and Carter), we would like to keep them.
‘At the end of the day, can we get those players on the terms which make financial sense?
‘If there’s deals to be done, we would very much like to do them.
‘However, if we can’t do a deal with those players it’s their prerogative .
‘We are sensible with every player, how that works within our structure and we have a clear idea on how we’ll use our budget.
‘Danny has identified the quality within the squad and those who are available with the quality coming through.
‘That’s how we structure things, otherwise we’ll utilise our resources without filling the key positions to bring the new players in who will make a difference.’