Rabiatou Serah Diallo, secretary-general of the National Confederation of Guinean Workers (CNTG).
"For the moment the meeting is cancelled.
"We asked for the lifting of martial law, security for union members, an end to night house searches and the carnage."
The unions are refusing to back Eugene Camara as a replacement for the 72-year-old Conte, claiming he is too close to the embattled president.
General Ibrahim Babangida, Nigeria's former military ruler, arrived in Guinea's coastal capital Conakry on Saturday at the head of a delegation from West African regional body ECOWAS.
"We wouldn't like to see Guinea get into a very chaotic situation. We have had previous experiences in Liberia and Sierra Leone," Babangida told journalists after meeting Conte.
"Guinea is a very important country within the sub-region. The leadership of ECOWAS wouldn't like to see that happen," Babangida said.
He said he was leading an "exploratory mission" and did not meet union representatives.
Human rights groups have criticised the imposition of martial law and the United States said on Friday it condemned "the abrogation of basic human freedoms."
The 53-nation African Union passed a resolution on Friday condemning the government for excessive use of force and called for an independent inquiry alongside with the African Commission of People and Human Rights.
Alseny Rene Gomez, Guinea's justice minister, rejected the call on Saturday, saying the West African state had already opened its own inquiry.
The unions have refused to take part in the inquiry.
"We cannot entrust something to the international community that we can do ourselves and that we have already started to do since January," Gomez said.
The US said in a statement that sending the military on to the streets of the country was not helping the volatile situation.
"The declaration of martial law and the accompanying restrictions on civil liberties are not conducive to the political dialogue that Guinea so desperately needs," the statement said.
Gabi Menezes, Al Jazeera's correspondent in Conakry, said: "Many people say that they are afraid to go out and face roadblocks manned by soldiers.
"But the government believes that if it relaxes the martial law, protesters will once again fill the streets."
More than 90 people, almost all civilians, were killed in an 18-day general strike against Conte's rule last month.