Hisham Marwa, deputy head of the coalition, which is recognised by much of the international community, dismissed the talks with UN envoy Staffan de Mistura as "unimportant".
And he said the body had been angered by de Mistura's decision to invite key regime ally Iran to the consultations.
"We were waiting for de Mistura to invite us to negotiations, and instead he invited us to unimportant consultations at a time when the Syrian opposition is winning key victories on the ground," Marwa told AFP.
"The invitation to Iran only strained the situation further and that's our basic problem with de Mistura," he added.
The UN envoy began talks last week with a wide range of parties involved in the Syrian conflict, including the Syrian government's envoy to Geneva.
The coalition had been expected to hold talks with de Mistura, who had described the consultations as a way to take stock of the situation more than four years into the conflict and potentially plot a path back to peace talks.
But Marwa said de Mistura's decision to invite some 40 "dissidents, artists, civil society organisations and research centres" to participate in the talks suggested he was not serious.
"It became clear to us that he does not treat the coalition in a way that gives the impression that he is serious about finding a solution."
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He also criticised the UN envoy for insisting that coalition chief Khaled Khoja attend the talks in person, rather than dispatching an envoy as Syria's government did.
Instead of participating in the consultations, a coalition member will travel to Geneva to deliver two letters addressed to de Mistura and UN chief Ban Ki-moon.
"The letters lay out our vision for a political solution as well as our observations on de Mistura's performance," Marwa said.
In Geneva, meanwhile, de Mistura said he had "taken note" of the coalition's decision and looked forward to receiving their envoy.
"Mr de Mistura is indeed interested in receiving the SOC (coalition) points of view on the Geneva consultations," a statement issued by his spokesperson said.
"This is indeed the whole purpose of the exercise in itself," de Mistura added.
More than 220,000 people have been killed in Syria since the country's conflict began in March 2011 with anti-government protests that spiralled into a war after a regime crackdown.
Several rounds of peace talks have made no headway, and de Mistura is the third UN envoy to tackle the conflict.