Villagers, along with government officials, say Vietnamese company Hong Anh Gai Lai (HAGL) did not have permission to fill in the lakes, which communities in the area considered culturally significant.
"[HAGL] violated the law. It was never approved by our administration. They did whatever they wanted, said Nguon Sokun, chief of the provincial Fisheries Administration, who received the complaint.
Villagers claim the lakes were filled in two years ago, work that also affected thousands of their cattle that relied on the lakes.
"We depended on those lakes during the dry and rainy season... Now we want the company to make other lakes for us, said May Chai, a village chief in Chey Uddom commune.
Chhay Thy, provincial coordinator for rights group Adhoc, said this was the second official complaint against the company that the community had brought forward.
In February, HAGL, which operates rubber plantations on economic land concessions, was accused by 17 indigenous families of land grabbing, prompting community representatives to file a complaint with the World Bank's International Finance Corporation (IFC), which is indirectly linked to HAGL through investments.
Last year, HAGL came under fire when Global Witness published a report titled Rubber Barons accusing it of illegally logging outside concession areas and being in possession of at least 47,000 hectares of economic land concessions - almost five times the legal limit.
Chang Vanveng, a translator employed by HAGL, denied the allegations on 24 June 2014, while Nguyen Van Thu, a representative for HAGL's operations in Cambodia declined to comment.
Source: Daily "The Phom Penh Post", Phom Penh; 25 June 2014 (Syed Rashid Ali, Karachi, Pakistan)