Sixteen people have died in the town since an aid convoy was allowed to enter the town earlier this month said MSF. This brings the number of residents reported to have died from starvation since December to 46.
The medical charity said that the real number "is almost certainly higher," adding that it has received reports of people starving in their homes.
Many more are in "danger of death" because of severe malnutrition, the humanitarian group warned.
Located in Damascus province, Madaya is under government siege and its fate has been one of the sticking points for fresh peace talks on the Syrian conflict that started in Geneva on Friday.
The Syrian opposition wants to see UN Security Council resolutions implemented that demand an end to the sieges in the country before committing to new negotiations.
Madaya was one of four towns included in a rare deal last year that was intended to halt fighting and allow the passage of humanitarian aid.
|It is totally unacceptable that people continue to die from starvation
- MSF's Director of Operations Brice de le Vingne
Despite the deal, the UN and other aid groups have only has limited access to Madaya, along with rebel-held Zabadani, and the government-held towns of Fuaa and Kafraya, which are under opposition siege.
Conditions in Madaya have reportedly been among the worst. Around 42,000 civilians are surrounded by government troops who have laid mines around the town to prevent them from leaving.
While the government has been able to airdrop supplies into Fuaa and Kafraya the opposition has no such capacity. Aid organisations have regularly urged continuous aid access to all four towns and called for the evacuation of those who are sick or suffering from malnutrition.
Citing medics it supports in the town, MSF said there were at least 320 cases of malnutrition in the town, including 33 that were so severe the individuals were likely to die without prompt treatment.
"It is totally unacceptable that people continue to die from starvation, and that critical medical cases remain in the town when they should have been evacuated weeks ago," said MSF's director of operations Brice de le Vingne.
"The warring parties responsible for these besiegement strategies need to allow unhindered medical and humanitarian access immediately," he added.
After the September deal for the four towns an initial aid delivery was made, but no assistance was allowed in until 11 January after reports of deaths in Madaya.
Additional convoys of food and medicine entered Madaya, Fuaa and Kafraya on 14 January, and all four towns received aid on 19 January.
However, aid groups have said the piecemeal deliveries are insufficient.
The UN estimates that over half a million Syrians are now living under sieges imposed by the regime, rebels or the Islamic State group.
The UN's humanitarian chief Stephen O'Brien said earlier this week that 75 percent of its requests for aid deliveries in Syria had gone unanswered by the government.