A police probe into his whereabouts has drawn a blank, and his family and friends believe he was abducted by government authorities who act against critics.
Eknaligoda was briefly detained, roughed up and freed by unknown assailants in August.
The family allege his current situation is linked to his support for defeated opposition presidential candidate General Sarath Fonseka.
"I believe high-ranking people within the government have abducted my husband for his writings and cartoons criticising President Mahinda Rajapakse," Sandhya Eknaligoda, 47, told AFP.
The government has denied the allegations, though the police admit there were problems in investigating Eknaligoda's disappearance as they were busy monitoring the presidential polls.
"There were some delays on our part to record the family's statements, but we are investigating his disappearance. We don't know where he is," police spokesman Prishantha Jayakody said.For Eknaligoda's family of two teenage boys, the greatest fear is that the 50-year-old journalist has been killed.
"I first thought that he'll be released in a day like the last time," said Eknaligoda's 16-year-old son Harith at the family home in Kottawa, a suburb of Colombo.
"Then we thought he would come home after the election. But it's over a month. I worry whether he is alive."
Eknaligoda was preparing an exhibition of his work this year and his sons proudly showed off dozens of framed cartoons, some of which lampoon ruling party politicians including President Rajapakse.
A few cartoons depict thugs wearing shawls similar to the trade-mark attire of Rajapakse, while one recent article Eknaligoda wrote about an unidentified minister's sexual misconduct is also thought to have contributed to his plight.
Sandhya says her husband actively campaigned for media freedom, taking part in public protests.
Having received verbal death threats and warnings that his telephone was tapped in the run-up to the elections, Prageeth appears to have been a marked man.
"He wrote and drew without fear. He is a multi-talented journalist. I pray he is safe, he is alive and he will be released soon," Sandaruwan Senadheera, editor of the Lankaenews.com website, told AFP.
Media and human rights groups have appealed for Eknaligoda's release and have criticised the government for persecuting journalists who are critical.
"Any government that subjects its independent news media to violent and arbitrary actions has no right to call itself democratic," said Commonwealth Journalists Association president Hassan Shahriar.
The Austrian-based International Press Institute (IPI) said Sri Lanka was one of the most dangerous places in the world for journalists to work with 17 killed in 10 years.
Two were killed in 2009. No one has been brought to justice in connection with the killings, IPI said.