In a 2016 research about working condition in the palm oil sector in Indonesia, Amnesty International investigated two plantations owned by subsidiaries of Wilmar (PT Perkebunan Milano and PT Daya Labuhan Indah) and three suppliers of Wilmar (PT Sarana Prima Multi Niaga, PT Hamparan Masawit Bangun Persada and PT Abdi Budi Mulia). The report states that workers have to meet (unrealistic) targets, otherwise their salary will be reduced and can end up below the minimum wage. The minimum wage in itself is not sufficient to meet living costs since the food at the remote plantations can be 40% - 50% higher in comparison to towns. The situation forces workers (at the investigated plantations) to get help from their spouses, children or others with their tasks at the plantation which results in child labour.

In December 2013 Wilmar adopted it's  ‘no deforestation, no peat, no exploitation’ (NDPE) policy, that required its suppliers to immediately cease any development of forests, including HCV (High Conservation Value) and HCS (High Carbon Stock) lands, and peat of any depth. However, several reports of NGOs have shown that Wilmar's suppliers or subsidiaries continue to engage in deforestation including HCV and HCS lands after their policy. 

In 2014 Greenomics found evidence that Kencana Agri, a company 20 percent owned by Wilmar, has engaged in deforestation in Sulawesi, Indonesia. Friends of the Earth Europe showed that Wilmar also continued to clear forest in the buffer zone of the Afi Wildlife Sanctuary in Nigeria, which contains HCV forest. In addition the report showed that Wilmar continued to purchase oil palm from the Indonesian company Bumitama Agri Ltd. which illegally cleared forest in critical orangutan habitat.

Another report of Greenomics showed that in the first quarter of 2015, Wilmar was buying CPO produced by PT Austindo Nusantara Jaya (ANJT), a company that continues to extensively clear high carbon stock (HCS) forest in West Papua province to date. According to a Mongabay article, Wilmar stopped sourcing from ANJT in April 2015.

Rainforest Action Network found that between June 2016 and January 2017 324 hectares of forest were cleared  in the Leuser Ecosystem (Sumatra, Indonesia) for an illegal plantation of PT Agra Bumi Niaga (ABN).  The palm oil from this plantation was transported to a nearby processing mill owned by PT. KPJ, which in turn provides crude palm oil to Wilmar.  Nestle said to be 'very concerned' about the allegation and Wilmar said to have put the purchases from ABN on hold. 

In June 2018 Greenpeace revealed that the company Gama Corp is run by senior Wilmar executives and members of their family. This means that Gama and Wilmar should be considered as one group according to RSPO rules and Indonesian Law. Gama has cleared an area of forest and peatlands twice the size of Paris in Papua New Guinea since Wilmar has announced its NDPE policy.  

In October 2014, the Nagari Kapa community, an indigenous community from West Sumatra, filed a formal complaint with the RSPO. The community accused Wilmar’s fully owned subsidiary Permata Hijau Pasaman I (PT PHP1) of taking over customary lands without Free Prior and Informed Consent of the Kapa people for the establishment of oil palm plantations. While the complaint was under investigation, PT PHP1 coninued to take over customary lands. In addition, community leaders were harassed and questioned about their involvement in the complaint with the RSPO by local police. In February 2017 the RSPO decided that Wilmar indeed had acted in violation of the RSPO sustainability standard.

Wilmar's fully owned subsidiary PT Bumi Sawit Kencana (PT BSK) is also involved in a land dispute in the Central Kalimantan Province in Indonesia. In June 2016 communities filed an official complaint with the RSPO for failure to pay compensation for the loss of land. The land dispute with citizens and PT BSK has caused several violent incidents, even resulting in injuries and the death of two villagers. 

In March 2018 Wilmar doubled its stake in the Ivorian firm SIFCA to 27.06%. SIFCA is running the Maryland Oil Palm Plantation. According to affected communities the project has caused desecration of sacred sites, destruction of crops and water resources and loss of land and livelihoods. In addition, community members say that state security forces were used by the plantation to silence dissents. 

Amnesty International has found discriminatory patterns at Wilmar’s subsidiaries PT Perkebunan Milano and PT Daya Labuhan Indah and its suppliers PT Hamparan Masawit Bangun Persada and PT Abdi Budi Mulia. With the exception of some women working in office administration, no women are giving permanent employment even though having worked for the companies for years, denying them access to benefits such as health insurance and pensions. 

Women are also often responsible for planting and maintaining the plants which requires them to use fertilizers and chemicals with the risk of health issues. When the rain washes away the used chemicals, workers have reported that they are payed only half a day or not at all because they have not met targets.