Singapore and Myanmar are both members of the 10-nation Association of Southeast Asian Nations (Asean), a regional body which has been criticised for tolerating human rights abuses by the Myanmar government and not pressing for reform.
Singapore, which is one of the biggest investors in Myanmar, has been a leading voice in opposing sanctions against the country and its rulers.
The city state is also believed to be home to much of the finances held in offshore bank accounts owned by the Myanmar military.
Call for prisoner release
Lee's remarks came as a UN investigator called on Myanmar's ruling generals to release more than 2,100 political prisoners and allow them to take part in an election set for 2010.
Tomas Ojea Quintana, the UN's special rapporteur on human rights in Myanmar, also urged the military to halt its use of civilians in forced labour.
Myanmar's military has ruled the country formerly known as Burma since 1962.
It refused to recognise a landslide victory of the opposition National League for Democracy in national elections held in 1990 and has jailed or detained many of its members including Aung San Suu Kyi, the party leader.
She has been under house arrest for most of the past two decades.
Western governments have criticised the government's plan to hold fresh elections in next year as a sham aimed at entrenching military rule.