The UN envoy had hoped to persuade Myanmar's military rulers to include opposition leader Aung San Suu Kyi and her National League for Democracy (NLD) party in plans for multi-party elections.
On Sunday Gambari held meetings with several mid-level ministers, a day after the government flatly rejected calls for international observers during a planned referendum.
The government also denied it was holding political prisoners and refused to free Aung San Suu Kyi, who has been held under house arrest for most of the past 18 years.
While the latest rejections were not unexpected, diplomats based in Myanmar said they signalled the end of whatever small desire the generals may have had to compromise.
Myanmar's military government has faced growing international condemnation after September's bloody crackdown on anti-government protests.
An Asian diplomat, who did not want to be named, said it showed "the regime has lost its appetite for co-operating with the UN".
Gambari arrived on Thursday on his third trip to Myanmar since the crackdown.
He met Aung San Suu Kyi on Saturday and again for 45 minutes on Monday morning, but has not been able to meet the country's top military ruler, Senior General Than Shwe.
According to the UN Information Centre in Myanmar's largest city, Yangon, Gambari met the ministers of health and national planning as well as the chairman of the civil service board and a deputy foreign minister on Sunday.
But the meetings did not appear to be related to political reconciliation efforts he was promoting.
On Saturday, the ruling generals rejected Gambari's call to let independent observers monitor the forthcoming national referendum on a new constitution.
Gambari had also sought to have the process for adopting a new constitution made more open to incorporate the views of the country's pro-democracy movement.
Asked by Gambari to consider releasing political prisoners - estimated by the UN and human rights groups to total more than 1,100 – the government denied that any political prisoners were being held in Myanmar.
It added that and that Aung San Suu Kyi had been detained because she tried to disrupt the country's stability.
The ruling generals announced last month that it would hold a referendum on a new constitution in May followed by a general election in 2010 in its "road map to democracy".
The plan has been dismissed by most Western governments as a blueprint for the generals keeping their grip on power.
Thaung Nyunt, the referendum commissioner, spurned Gambari's offer of UN "technical assistance", saying the military had enough experience with running elections.
The last time it did so, in 1990, it ignored the result which gave the NLD more than 80 per cent of the vote.
State media has said that under the rules for the planned elections, Aung San Suu Kyi will not be eligible to run because her late husband was a foreigner.
The NLD's ability to campaign in the 2010 elections will also be limited, although the military called on Gambari to encourage the party to take part in the polls.