Cottonsoft's four retail brands have certification under the independent PEFC (Programme for the Endorsement of Forest Certification), the world's largest forest certification programme, he said.
He said Cottonsoft did not participate in Greenpeace's survey in part because it was unable to promise the information would be treated as commercially sensitive.
Cottonsoft is a subsidiary of Asia Pulp and Paper (APP).
"APP conserves rare and endangered species, and places the protection of species, such as the Sumatran tiger, at the heart of its operational and CSR policies. Of the area that APP controls, which constitutes 1.5 per cent of Indonesia's landmass, 40 per cent is set aside for conservation," Mr Nicholson said.
All raw materials sourced from Indonesia complied with fundamental International Labour Organization Conventions in forest management, he said.
"The unfounded attack on our New Zealand business endangers the job security of Cottonsoft's 130 New Zealand employees in its Auckland and Dunedin plants. That people should be at risk of losing their jobs and having their financial stability threatened because of erroneous allegations is outrageous."
APP also supported a tiger protection scheme, and recently moved an at-risk tiger from an area of animal/human conflict to a nature reserve, he said.
Indonesia was the largest supplier of imported toilet paper pulp in New Zealand and made up one in every four rolls used by New Zealanders, the groups' investigation said.
WWF executive director Chris Howe said many New Zealanders would want to make sure their shopping choices were not harming forests and wildlife in Indonesia.
"We encourage people to help ensure the forest homes of endangered tigers and orangutans remain in tact by using the consumer guide to make the right choice at the checkout."
Indonesia has one of the fastest rates of forest destruction in the world with the Indonesian government estimating more than one million hectares of rainforest were being cleared every year. Rainforest destruction is also acknowledged as a major driver of climate change.
The destruction of Indonesia's rainforests is one of the main threats to the survival of the critically endangered Sumatran tiger, only 400 of which are estimated to remain in the wild.
- NZPA