The Greek champions were forced to sit out a second round of fixtures this weekend in a campaign being delayed because only 14 of the 16 teams have been confirmed to play in the top flight due to legal disputes after a match-fixing scandal.
"Our official matches start with the [Group F] game against Marseille in the first match of the Champions League and this is difficult for us," manager Ernesto Valverde said on the club website.
"It is a great concern [that Olympiakos have not played a competitive match yet], as well as the departure of Riera," said Valverde.
"He was a key member of the team and there is a huge void to fill but we cannot cry about it. I prefer to work with players who want to be at this football club."
The EEA's examination of the applications of the two second division clubs is expected to conclude next week.
Goals from Spaniards Josu Sarriegi and Toche put the Greens 2-0 up before striker Ibrahima Bakayoko's 65th-minute effort gave Giannena hope.
Panathinaikos' Argentine winger Sebastian Leto struck with 15 minutes left, however, to calm the hosts' nerves and seal the three points for Jesualdo Ferreira's men, who top the fledgling Super League table after two matches.
