Aid agency Pharmaciens Sans Frontières (PSF), or Pharmacists Without Borders, said donated medicines have created more problems for the government than benefits for the victims.
Donors sent medical aid to the region after the 2004 Indian Ocean tsunami which killed 168,000 people in Aceh province and an earthquake on Java in May that claimed some 5,800 lives.
"It's a second tsunami, a huge wave of drugs donations that authorities are totally unable to handle," PSF pharmacist Laurence Boiron said, referring to some 600 tons of expired, damaged or inappropriate medicine sent to Aceh.
Some 200 tons of unusable drugs taken from Nias Island, hit by a deadly earthquake in March last year, are to be incinerated on Friday at a cement factory in Bogor, south of the Indonesian capital Jakarta.
In early July, 150 tons of drugs donated to Aceh were burned and there are plans to destroy another 50 tons of donations which arrived after the Yogyakarta earthquake on May 27.
The World Health Organisation has set strict guidelines for donated drugs. They must comply with the WHO official list of approved medicine, be in use in the receiving country and have, upon arrival, a remaining shelf life of at least one year.
But the guidelines are frequently ignored. In Aceh, 70% of donated drugs were labelled in a foreign language other than English or Indonesian, contrary to another WHO guideline.
"Countries such as Poland, China, South Korea or Spain are regulars when it comes to single-language labelling," said Sylvain Denarie, a WHO supply manager in Jakarta.
Banda Aceh hospital's pharmacist Abu Sa'adi recalled receiving cases of injectable Pantozol, a drug used to treat gastritis.
"But in Indonesia we only use it in tablets, so doctors had never seen these. We didn't use them in fear of killing patients," he said.
The eventual cost of dealing with the drugs can easily outstrip their usefulness.
"With a cost of $250 per ton to incinerate, we could (instead) be building a health centre," said Astrid Kartika, a health adviser for the United Nations Development Programme which is organising and paying for Friday's incineration.
The drugs also pose a threat to the environment if stored over a long period of time and many end up on the local black market, experts said.
"Between the time we finished identifying the drugs and the moment we closed the warehouse to take them to the cement factory - that is, four months - 250 tons of unusable drugs vanished in thin air," PSF's Boiron said.
Bahron Arifin from the Indonesian ministry of health added that the government never asked donors for drugs when the 2004 tsunami first hit.
"What we need in times of emergency are blankets, shelters and food," he said. "Drugs, we have enough of them here."