Lee Young-ryeol, the senior prosecutor directing the probe, said on Sunday 53 conglomerates, "fearing direct and indirect drawbacks to business activities such as tax audits", were "coerced to contribute funds" to the foundations.
Park Ju-gun, head of research firm CEO Score, said there was little surprise that prosecutors were now seeking evidence in Samsung Group offices about how the merger may have been influenced by the conglomerate's contributions to the foundations.
The merger of the Samsung affiliates was approved by shareholders in July 2015 and prosecutors said the two foundations involved were set up in the following six months.
"This was expected. Due to the circumstances in this case, prosecutors cannot help but be suspicious about the genuine intent behind the donation, such as the timing," CEO Score's Park said.
President Park, through her lawyer, has pushed back on a request by prosecutors to question her about the case, potentially the first time a sitting South Korean president would be interrogated in a criminal case.
Park, who's five-year term ends in February 2018, has resisted calls to resign but has apologised twice, saying she only sought to benefit the economy and not herself, but acknowledges carelessness in her ties with Choi.
However, the growing calls for her to resign and Park's virtual withdrawal from public activities has left a worrying power vacuum in South Korea.
Choi and former presidential aide An Chong-bum were indicted on Sunday and charged with abuse of power, a major blow to the president's fight for political survival.
NPS has defended its decision in the face of criticism that the deal helped the Samsung Group family to cement control of the merged firms at the expense of other shareholders.
"The reason we approved the merger was due to taking a comprehensive view of the merger's synergy effect and potential for stock value increase," it said in a statement last week.
There were "special circumstances" where NPS-owned stakes in both firms were valued at a similar amount, it said. The size of NPS' combined stakes in both firms was about 2.4 trillion won ($2.05 billion), or 3 percent of NPS' domestic stock portfolio.
However, according to records of the NPS Investment Office committee's decision to back the merger in July 2015, acquired by an opposition lawmaker and seen by Reuters, the NPS had calculated a merger ratio of 1:0.46 of Cheil Industries shares to Samsung C&T shares, based on its valuations of the two firms.
This differed from Samsung Group's proposed ratio of 1:0.35, which the NPS committee noted was comparatively unfavourable to Samsung C&T shareholders.