The Red Sea FC players were due to leave the country on Saturday after their elimination from the Cecafa club championship at the semi-final stage but a head count at their departure point revealed that half the squad were missing.
"Thirteen out of 26 players of the Eritrean team have disappeared," secretary general of the Tanzania Football Federation (TFF) Angetile Osiah told Reuters.
"We have reported the matter to relevant law enforcement authorities for investigation.
"Some team members colluded in the incident by trying to stamp the passports of the missing players at airport immigration checkpoints but when a physical head count was conducted, it was discovered that 13 players were missing."
Illegal immigrants from Ethiopia, Eritrea and Somalia often use the east African country as a transit point to South Africa and elsewhere.
It is not the first time members of an Eritrean team have vanished after a tournament outside the country. In 2009, 12 members of the national squad disappeared in Kenya after competing in a regional tournament.
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