An offer by Gambari for the UN to provide technical expertise for the vote was also rejected, the reports said, with the government explaining that it had sufficient resources to hold the polls on its own.
Brigadier-General Kyaw Hsan, the information minister, accused Gambari of bias in favour of Suu Kyi, criticising him for releasing a letter from her after his last visit in November.
He told Gambari during more than two hours of talks on Friday that the government would not make any changes to the proposed charter.
"The constitution has already been drafted and it should not be amended again," Kyaw Hsan, whose lengthy comments were reported in detail by state media, said.
"We are very astonished and dismayed for your involvement in this matter," he said in the official New Light of Myanmar newspaper.
"Sadly, you went beyond your mandate. The majority of people are criticising it as a biased act.
"Some even believe that you prepared the statement in advance and released it after co-ordinating with Daw Aung San Suu Kyi."
He added that if Gambari tried to force the country to meet Western calls for reform, "we are concerned that your task of offering impartial advice may be undermined".
The comments appeared to dash any hopes that the government would make concessions in its election plan.
A spokesman for Suu Kyi's National League for Democracy (NLD) party, which won a 1990 election only to be denied power by the army, declined to elaborate on the content of her talks in Yangon with the Nigerian diplomat.
The NLD has warned that the public would not accept the military government's new charter, but it has stopped short of calling for a boycott or urging a "no" vote.
Suu Kyi was taken to and from the meeting in a convoy that picked her up at her house in Yangon, where the 62-year-old Nobel peace prize winner has spent 12 of the past 18 years under arrest.
Officials declined to provide any information about their talks. Normally Gambari only discusses his meetings after leaving the country.
The UN envoy earlier held talks with officials from a pro-junta party and a civil group set up by the government known as the Union Solidarity and Development Association (USDA).
Gambari arrived on Thursday on his third trip to Myanmar since the deadly crackdown on non-violent pro-democracy protesters in September sparked a global outcry.
Media reports said Gambari's idea was rejected because there was no precedent for it and it infringed on Myanmar's sovereignty.
The visit came amid growing concerns that the government is ignoring calls for political reform and is tightening its grip on power.
The new constitution would bar Suu Kyi from future elections because of her marriage to a foreigner, the late Briton Michael Aris.
A new law governing the referendum also limits her party's ability to campaign by criminalising public speeches.
The military government said last month that it would hold a constitutional referendum in May and general elections in 2010 - the first specific dates for steps in a previously announced "roadmap to democracy".
Dissidents, diplomats and human rights groups have dismissed the roadmap as a sham designed to allow the perpetuation of military rule.