Niger's human rights commission has called for an independent inquiry following alleged rapes, including that of an 11-year old girl, by Chadian soldiers deployed in the west African country to help fight Islamist militants.

The commission's preliminary findings, published on Friday and based on testimonies and medical examinations between March 31 and April 1, were that two other women were raped.

The women, including one who is pregnant, were raped in the presence of their husbands who were held at gunpoint by the soldiers, according to the commission's report.

"Other rape victims refused to testify due to fear of being stigmatised," the report said, adding that the commission spoke with five women who were victims of attempted rape, having managed to flee when armed men entered their homes.

Chad's government spokesman did not answer when reached for comment. Chad's defence ministry, and the government of Niger were not immediately available to comment.

France and other allies praised Chad in February after it deployed 1,200 troops to the tri-border region between Niger, Burkina Faso and Mali to reinforce 5,100 French soldiers battling militants linked to al Qaeda and the Islamic State.

Besides the alleged rape cases, the report noted that Chadian troops have also been accused of assault and confiscation of private properties in the Tera region in the west of the country near the Burkina Faso border where they are deployed.