The club faced liquidation towards the end of last season, and their eventual relegation has left the squad in need of a major overhaul, with several linked to moves elsewhere
Just eight senior players turned up for the session on Monday, and Pompey boss Michael Appleton now faces a tough job.
"I was expecting 10 at training, but there were a couple of absentees," Appleton told BBC Radio Solent.
"If I was a betting man. I'm guessing one is in Nigeria [Kanu] and the other is in South Africa [Mokoena]."
Appleton was unsure where Kanu and Mokoena were at the time of the training session, but believes that they are unlikely to play for the club again.
"We are very close to an agreement with Aaron. Regarding Kanu, who knows?
"I think there has been a conversation between Kanu's solicitors and [administrator] Trevor Birch, but I'll leave that to them to sort out. I doubt very much they'll be back."
Kanu has made 167 appearances for the South-Coast club since joining from West Brom in 2006, while Mokoena has played 89 times following his arrival from Blackburn in 2009.
Appleton admits after a summer littered with financial worries he was glad to return to action.
"It was a sigh relief to get back to training," he added.
"It was an interesting experience only having eight senior players turn up for training. They came back in reasonable shape and gave it a good crack."Luke Varney and David Norris are also likely to leave the club, but Ashley Westwood's arrival as first-team coach has stalled.
Appleton expects the potential transfers to happen before the start of the season, but financial troubles have meant that bringing in replacements has proven difficult.
"I think they have been in contact with the clubs and over the coming days I would imagine Luke and David would get themselves sorted and we'll move forward from there," said Appleton.
"We still need bodies to leave the building before we can bring people in.
"Everything has been agreed with Lincoln [for Westwood,] but at the minute I don't expect anything to be finalised until the end of the week."
Appleton also revealed that ex-Chelsea man John Harley was on trial at the club.