The Mexican government has found no evidence to confirm a priest's report that at least 80 Central American migrants were kidnapped from a freight train last week, according to an official.

The interior department's deputy secretary, Rene Zenteno, said two witnesses from Honduras and Guatemala told federal investigators they saw gunmen get off the train and take two women, two men and a child with them.

No evidence or testimony of a larger kidnapping had been found, Zenteno said.

The Rev Alejandro Solalinde, who manages a migrant shelter in Oaxaca state, had reported that witnesses told him more than 80 migrants were abducted in neighbouring Veracruz state by gunmen who hijacked the freight train on which they were travelling last Friday.

Solalinde told Radio Formula that witnesses told him the gunmen forced migrants to climb down from the top of the cars and bundled some into at least three waiting SUVs.

"What [the witnesses interviewed by authorities] saw were the first five get in the cars, but they are not the only ones … do you think they would need three SUVs for five people?" Solalinde said.

Zenteno said that if the priest had more evidence, he should give it to authorities.

"He's assuming that they were kidnapped because they got on the train," Zenteno said.

In December, Solalinde reported that about 30 migrants were taken from a train in Oaxaca state. Mexican authorities initially said they had no evidence the kidnapping had taken place but eventually arrested five people.

Thousands of Central American migrants enter Mexican territory without permission each year, most bound for the US.

A report released in February by Mexico's National Human Rights Commission said at least 11,333 migrants were abducted between April and September 2010.

Zenteno said authorities had rescued more than 4,000 migrants since January and arrested 147 alleged migrant traffickers. Most of the migrants were rescued in the northern state of Tamaulipas, across the border from Texas.

One of the worst attacks against migrants in recent history occurred in Tamaulipas last August, when 72 migrants were killed in the town of San Fernando. The Zetas drug cartel is suspected in the killings.

The foreign relations department said on Wednesday that it had been in communication with El Salvador, Guatemala and Honduras "to facilitate the flow of information in the case of the alleged mass kidnapping".