The extremists separated the Christians from the Muslims, asking them questions about Islam and the Quran, before taking them.
In April, Islamic State kidnapped 79 Eritrean and Ethiopian Christians in Libya, before releasing a video showing the group murder 30 of them days later. There are concerns Islamic State will do the same with the latest kidnapped refugees.
Meron Estafanos, a journalist and activist who directs the Eritrean Initiative on Human Rights, confirmed the news after some migrants who escaped telephoned her describing the situation. Nine refugees escaped the latest Islamic State attack, according to Mrs Estafanos.
She told Premier: "On Thursday night then I received a phone call from three that have managed to escape actually from Isis. I mean they still are in the middle of nowhere and they were afraid and they said 'we just escaped and we don't know where to go', because there is no help for them and they don't want to tell people they have escaped from Isis because nobody will help them.
"So some [Christians] that grew up in Sudan, it's easy for them [to pretend to be Muslims] because they know the [Islamic] prayer, so they did say that they were Muslims, but others, they couldn't. They [Islamic State] asked them questions and then they had to show the prayer, how you pray from the Quran, and most of them couldn't, so they took them.
"It has always been dangerous [to be a Christian in Eritrea] actually to be honest. I receive phone calls from many refugees that would tell me they've been discriminated because of their religion, especially during the Ramadan time.
"It's the worst time because you're not Muslim but you're forced to fast just like others, they'll refuse to give you food, and once its time to eat then they'll give you less food because you're not Muslim."
Listen to Premier's Aaron James speaking to Meron Estafanos: