The department of homeland security has agreed to consider same-sex partners as being in a "family relationship" during immigration proceedings, in a move that may spare undocumented immigrants in long-term partnerships with US citizens the grief of forced separation.

The concession, enshrined in writing in a letter from the DHS secretary, Janet Napolitano, softens one of the most bitterly resented aspects of the Defence of Marriage Act (DOMA), the 1996 federal law that defines marriage as the union of a man and woman. Under DOMA, immigration rights that are extended to bi-national heterosexual couples are not similarly offered to gays and lesbians.

"One of the most painful aspects of the Defence of Marriage Act is when couples are separated. So we are happy to see the DHS acting on this," said Victoria Neilson, legal director of Immigration Equality, a group that advocates for changes in US immigration laws relating to the LGBT community.

Napolitano's letter is the latest move by the Obama administration to use its procedural powers to ameliorate some of the harshest aspects of immigration law without having to face political opposition in Congress. In June the administration allowed young undocumented immigrants who had come to the US as children and were in education to apply for a deferral of any threat of deportation for two years. More than 80,000 people have applied for deferred action so far.

The procedural shift on deportations of gay partners is much smaller in its likely reach. It is estimated that there are about 24,000 gay and lesbian couples in the US where one partner is a national of another country, though how many of those are without immigration authorisation is not known.

The DHS has been saying for more than a year that it wanted to focus its resources on priority cases for deportation, such as those with criminal records. It has made clear that it would treat favourably anyone with strong family or community ties in the US, though until now it left the status of gay relationships unclear.

Napolitano's letter removes the ambiguity. She writes that guidance will now be sent to all immigration officers in the field, to clarify for them that "family relationships includes long-term, same-sex partners".

The DHS secretary has been coming under mounting pressure to do something about the status of gay couples facing immigration problems. In July, a group of 84 members of Congress wrote to her, asking her to put into writing the equal position of gay couples in terms of deportation proceedings.

One of the authors, Michael Honda of California, told NBC News: "No one should have to choose between their spouse and their country, and no family should be left out of the immigration system."

Immigration Equality has tried to persuade the DHS to grant what would in effect be temporary visas to undocumented immigrants. DOMA prohibits LGBT partners of American citizens from applying for green cards that would grant them resident status.

Under the Immigration Equality proposal, people could apply for the cards and their applications would then be put on hold, pending the repeal of DOMA which the Obama administration has indicated it supports. While their applications were on hold they would be granted temporary permission to stay in the country, although they would not have the right to work.

The DHS, however, has indicated that it is not likely to implement such a proposal.