Paulsen also questioned NST's professionalism in quoting International Movement for a Just World (JUST) president Professor Dr Chandra Muzaffar as saying NED assistance was handed out with the objective of stirring up people and that contributions had hidden agendas.
"If NST had been a proper media organisation with integrity, why didn't they ask Chandra Muzaffar about his track record or where he receives funding?” he asked.
Most of the organisations named in the article deal with public interest issues. Lawyers for Liberty deals with cases of police shooting and brutality.
“We are pro-democracy and support electoral reform, but somehow that's always linked to being anti-government,” added Paulsen.
Related story: NGOs hold press conference to deny claims
Malaysiakini chief executive officer Premesh Chandran explained that the portal receives grants not just from NED but also from other international donors to support its special projects.
Aside from Seacem, the grants helped Malaysiakini build a team of 300 citizen journalists from across the country and set up information sites such as Undi.info and digitalibrary.my.
"We're happy to work with international foundations on interesting projects to promote press freedom. We are transparent about such partnerships. These grants form a small part of Malaysiakini's budget,” he said.
Representatives from Suaram, SEAPA and Liberal Banter Sdn Bhd also told Yahoo! Malaysia that NST had not contacted them for their response to Chandra's allegations.
The NED website states that it is funded largely by the US Congress and was created jointly by the Republicans and Democrats, with both parties having representation on its board.
The NED also posts all its grant recipients and activities on its site and is subjected to multiple layers of oversight by the Congress, the Department of State and independent financial audits.
Ambiga had, in a June report from The Malaysian Insider, admitted to receiving funding from two US organisations — the National Democratic Institute (NDI) and Open Society Institute (OSI) for projects that were unrelated to the July 9 rally. NDI is named in the NST article as an NED fund recipient.
A smaller article, making similar allegations, was also carried on page six of Friday's edition of The Star.
This is not the first time that NGOS have been questioned about their funding sources. In 1999, Malaysia's former Foreign Minister Syed Hamid Albar pointed out that the government objected to foreign funding for political parties and NGOS prior to the 10th General Elections.
He had said the government considered moral and financial support from foreign missions to local parties and NGOS unacceptable and were “acts of interference”.