The junta has rebuffed repeated requests by foreign diplomats to meet Suu Kyi and her lawyers were barred from speaking to the media for much of her trial.
She was transferred from house arrest in Naypyidaw to solitary confinement in prison in June last year.
Manalo said it was "good to hear" that Suu Kyi was in good health because "she used to attend our meetings".
The two-day Association of Southeast Asian Nations meeting has been dominated by the crisis, which has left the bloc divided about how and whether it should re-engage with Myanmar's junta rulers.
They have been barred from ASEAN's high-level meetings but Thailand hosted the junta's foreign minister last month for controversial "informal talks" that further split the bloc.
ASEAN chair Indonesia and Malaysia did not attend but Cambodia sent a foreign ministry official.
Don said he was advocating for "engagement with the authority in Naypyidaw" to bring an end to the crisis.
"Obviously, we are trying to find a way to settle Myanmar. After two years, there's a development and that should be... positive," he said.
Indonesian Foreign Minister Retno Marsudi told her counterparts on Wednesday "only a political solution will lead to a durable peace" in Myanmar.
Ministers were still hammering out a joint position on Myanmar on the second day of talks but a joint communique was expected by the end of the day, a Southeast Asian diplomat told AFP.
One day visit
Don "visited here just for a day trip and met with the commander in chief" Min Aung Hlaing, a senior Myanmar military official told AFP on condition of anonymity.
"I didn't know about any meeting with Daw Aung San Suu Kyi," he said, using a Burmese honorific and without detailing when Don had visited Myanmar.
The military has cited alleged widespread voter fraud during elections in November 2020 as a reason for its coup, which sparked huge protests and a bloody crackdown.
Those polls were won resoundingly by Suu Kyi's National League for Democracy.
International observers said at the time the polls were largely free and fair.
The NLD was devastated by the coup, with many senior members jailed or sent into hiding.
Myanmar has been in turmoil since, with the junta razing villages and conducting mass extrajudicial killings and air strikes on civilians, according to rights groups.
More than one million people have been displaced by fighting between the junta and opponents of the coup, according to the United Nations.