Lienen was upset by what appeared to be an offside in the build-up to Marama Vahirua's second-half goal and thought they deserved a penalty when Michalis Pavlis was felled by Deniz Baykara.
The result left AEK with 11 points, a point behind Aris Salonika, Kerkyra and Veria who all drew at the weekend.
"I have been a coach for many years and I have never spoken about referees but no team should lose because of a referee," a furious Lienen said.
"The referee really hurt my team today, he should be ashamed of the decisions he made. Nothing but shame," the 58-year-old added.
Lienen, who replaced Vangelis Vlachos on Oct. 10 after AEK's worst start to a top flight campaign, helped haul his team off the bottom with a 2-1 home win over PAS Giannena last Monday.
The cash-strapped club were forced to sell almost their entire first team squad in the close season to secure a licence to play in the Super League.