Ms Truss walked on to the stage to the 1993 hit Moving On Up before she delivered her keynote speech to party members in Birmingham, England.
Mike Pickering, who wrote the song, said on Twitter that the band was livid over the selection and claimed he had not given permission for its use.
"Hopefully most people will know that they have pirated it off us," he said. "She won’t be around to use it again for very long, I would imagine.”
Pickering said the band had contacted their lawyers but had been advised there was little that could be done.
He also mentioned that the band's lead vocalist, Heather Small, had a son who was active in the Labour Party.
The dance anthem, which was released by the Manchester band, peaked at number two on the UK singles chart.
Ms Truss is understood to have personally selected the song for her walk-on music.
“There was a range of options and she chose that one,” her press secretary said, but could not say whether the party had asked the band for permission.
“I don’t have detailed knowledge of how the licensing of this stuff works,” he told PA.
When asked about Pickering’s criticism, the press secretary said: “I don’t know who he is.”
Pickering said that he was "gutted" and that the Tory Party were "killing the live touring of bands and artists" following Brexit.
Pickering also suggested that the track was an unusual selection and that the Tory party had not taken proper notice of the lyrics.
He told PA: “I was just looking at the lyrics. It’s amazing. I hope she takes note. It’s about, ‘Go and pack your bags and get out’."
Ms Truss entered to the track’s famous chorus “Movin’ on up, nothin’ can stop me. Movin’ on up, you’re movin’ on out. Time to break free, nothing can stop me.”
The opening lyrics of the song read: “You’ve done me wrong, your time is up”, with the last line of the first verse saying: “Move right out of here, baby, go on pack your bags”.
James Small-Edwards, the son of the group’s lead singer, Heather Small, was elected as a Labour councillor for Bayswater, west London, in May.
After Ms Truss’s entrance, he tweeted: “An apt choice! This tired and out of touch Tory government is indeed moving on out.”
Mr Small has also previously shown his support for refugee charity Care 4 Calais’s #StopRwanda campaign.
Boris Johnson used Friendly Fires’ track Blue Cassette as he walked out for the party conference last year.
The indie band later hit out at the prime minister, saying their “permission was not sought” to use the song and that they had asked their management to ensure it was not to be used again by the party.