All football matches, including the domestic league, have been suspended indefinitely following the screening of an investigative documentary which exposed corrupt and match-fixing activities of top Ghana Football Association officials and referees.
For the Porcupine Warriors, the break was ill-timed as they looked to be finding their rhythm after a challenging start to the season.
"We really miss the league," Annan told Virgin FM.
"On the part of Kotoko, we were getting back to our form and the team was taking shape before the break of the league.
"It is very worrisome [and] we've been discussing it among ourselves.
"We feel things would have gone well for us should the league be going on.
"We just hope and pray everything settles down for us to return to our game."
Kotoko currently sit fourth on the league table after 15 rounds of matches, having won seven, drawn three and lost five times.
It is unclear when the topflight will return with the ban still in force.
A Ghanaian delegation will meet with Fifa in Zurich on Friday to discuss the way forward for the country’s football.