The National Guard in the US states of Texas and Mississippi have refused to process benefits requests from Tuesday from same-sex couples, despite a directive from the Pentagon to do so.

Tuesday saw the benefits kick in. The Defense Department had announced that couples in same-sex marriages performed in states where it is legal would be recognised as legally married, following the Supreme Court’s ruling on the Defense of Marriage Act (DOMA), back in June.

Yesterday also saw the first day on which military service members could apply for special leave of up to ten days to allow same-sex couples to travel to a US state where equal marriage is legal, in order to marry.

Both Texas and Mississippi cited their state-wide bans on same-sex marriage in refusing to process applications for the benefits, however they appeared to be the only two to have refused, reports the Associated Press. The 13 other states which also ban equal marriage said on Tuesday that they would process the applications.

The AP obtained a letter from Major General John Nichols, the commanding general of Texas Military Forces, saying that because of the state constitution defining marriage as between one man and one woman, his agency would not process applications from gay and lesbian couples.

He continued to say that the Texas National Guard, Texas Air Guard and the Texas State Guard would not deny anyone benefits, as they could apply at a federal installation, and listed 22 bases operated by the Defense Department where same-sex couples could enrol.

Nichols said that his agency, which oversees National Guard Units “remains committed to ensuring its military personnel and their families receive the benefits to which they are entitled. As such, we encourage anyone affected by this issue to enroll for benefits at a federal installation.”

Texas Governor Rick Perry weighed in to say that Texas Military Forces, as an agency of the state, must obey state law.

Mississippi National Guard spokesman Tim Powell said, similar to Texas, the main factor in determining whether same-sex spouses could apply for the benefits was down to whether a base was on federal property, or state-owned.

“It is our intent to provide benefits and services to our men and women in uniform and at the same time abide by federal and state statutes,” Powell said.

The American Military Partner Association, an advocacy group for LGBT military families, obtained the letter from Nichols, and condemned the decision not to offer the benefits.

“It’s truly outrageous that the State of Texas has decided to play politics with our military families,” said Stephen Peters, the president of the association.

“Our military families are already dealing with enough problems and the last thing they need is more discrimination from the state of Texas.”