Ban said military supremo Than Shwe had not yet granted him permission to see the 64-year-old opposition leader but added that he awaited a final reply before his two-day mission ends on Saturday.
The UN chief flew to Naypyidaw, the remote stronghold of the regime, shortly after a prison court again adjourned the widely condemned trial of Aung San Suu Kyi on charges of breaching the terms of her house arrest.
"I told him that I wanted to meet her in person. He told me that she is on trial but I told him this is my proposal, this is important and I am waiting for their consideration and reply," Ban told reporters after the talks.
Than Shwe appeared in his olive green military uniform at the start of the meeting but did not speak.
Asked how soon he expected a response from the junta on his request to see her, Ban said with a smile: "I am leaving tomorrow, so logically speaking I am waiting for a reply before my departure."
Ban said he had also sought the release of the more than 2,000 political prisoners that the UN says are held in Myanmar -- including Aung San Suu Kyi -- ahead of elections promised by the ruling generals in 2010.
"I proposed and I urged that all political prisoners should be released before this election begins, so that this election can be all inclusive," Ban said.
The 64-year-old Aung San Suu Kyi was transferred from house arrest to Yangon's notorious Insein prison in May on charges of violating her house arrest, after an American man swam uninvited to her lakeside house.
She has spent most of the past two decades in detention and now faces five years imprisonment if convicted.
Ban said earlier that it was a "very tough" mission.
Rights groups warn that the trip will be a "huge failure" if he does not secure the release of Aung San Suu Kyi. Critics have accused the junta of using the trial to keep her locked up for the elections.
She appeared in court Friday but the trial was adjourned for a week because the judges had not received an earlier judgement barring two defence witnesses, said Nyan Win, spokesman for her National League for Democracy (NLD).
The case has sparked international outrage, with US President Barack Obama calling it a "show trial" and a host of world leaders and celebrities calling for her release.
Ban earlier made an apparent reference to concerns over the timing of his visit while her trial is under way, saying he was aware that he was coming to Myanmar "under certain uncertainties."
He was due to meet representatives of all registered political parties and former armed groups while in Naypyidaw.
Ban has faced recent criticism for his softly-softly approach to the job of secretary general, but diplomats say he hopes his quiet brand of diplomacy will pay dividends with Myanmar's generals.
The visit is Ban's first to Myanmar since he persuaded the junta to accept international aid following Cyclone Nargis in May 2008, which killed around 138,000 people.
Aung San Suu Kyi has been in detention or under house arrest for 13 of the past 19 years since the junta refused to recognise the NLD's victory in Myanmar's last elections, in 1990.
Human Rights Watch said on Thursday that Ban should not accept the apparent concession from the junta of returning her to house arrest, instead of imprisoning her, as a sign of a successful visit.
"Time and again, the UN has politely requested Aung San Suu Kyi's release, but her 'release' back to house arrest would be a huge failure," said Kenneth Roth, New York-based HRW's executive director.
Myanmar, formerly known as Burma, has been ruled by the military since 1962.