The probe follows revelations by the Central Bank of Samoa on Thursday that the cryptocurrency OneCoin had "compromised" Samoa's financial system.
Citing a report it was handed by New Zealand police, the Central Bank said OneCoin - also known as OneLife - had used two Samoan churches with branches in New Zealand and Australia to funnel millions of dollars into Samoa.
The Central Bank's acting-governor, Gilbert Wongsin, told RNZ Pacific on Tuesday there were active investigations into the Samoa Worship Centre and the Samoan Independent Seventh Day Adventist Church.
"We have liased with police in terms of the information that we have," he said in a phone interview, adding that the probes would seek to establish whether the churches breached anti-money laundering laws in Samoa.
The Central Bank last week labelled OneCoin a "hybrid ponzi-pyramid scheme" which had implicated a number of Samoan individuals and money transfer operators. In the interview, Mr Wongsin said hundreds of Samoans had invested in OneCoin.
A pastor with the Samoa Worship Centre in Apia, Josh Seiuli, said lawyers for the church were exploring possible legal action against the Samoan government over defamation.
"Honest to god, we never done any transfer or any transfer action using Worship Centre accounts," he said, adding that around 500 Worship Centre parishioners in Samoa had invested in OneCoin.
Mr Seiuli said most people - including himself - had not broken the law because they had invested before the Central Bank imposed a ban on OneCoin transactions last May.
An Auckland-based minister with the Samoan Independent Seventh Day Adventist Church, Fa'avae Gagamoe, declined to comment.
Money laundering carries a maximum penalty in Samoa of 15 years imprisonment, a maximum fine of around $US374,000 or a combination of both.
Mr Wongsin, the Central Bank's acting-governor, said Samoan authorities were considering possible action against OneCoin, but declined to elaborate.
The Bulgaria-based company has not responded to multiple requests for comment since Thursday but in March said transparency was one of its core values.
Mr Wongsin said authorities were also still working on what action to take against Samoans implicated in the scheme.
"It's something that people need to have a good understanding of what it is all about. This is one of the efforts that the Central Bank is working on. To make sure that not only the people of Samoa but the financial system is not exploited."
According to one expert, OneCoin had exploited the vulnerability of church-centred communities in the Pacific and abused the trust placed in ministers and pastors to sell their product quickly.
"In these communities there is an enhanced sense of family and community bonds and with that comes a very strong sense of trust. And of course, trust can be exploited by these scams," said Campbell Pentney, a senior associate at Auckland law firm Bell Gully.
In interviews, Samoa Worship Centre members said before the ban was imposed the church was used to facilitate presentations from OneCoin company representatives to parishioners.
IT engineer Fono Toluono said he was a OneCoin "independent marketing associate", or IMA, an internal qualification which enabled him to onsell the cryptocurrency.
Mr Tuluono, who has invested around $US1100 in the scheme, said he had encouraged a lot of Samoans to invest.
"I pointed the people to the website so they can sign up, because everything was on the website to buy the package."
The pastor, Mr Seiuli, said he also assisted with congregation members who wanted to invest, including answering questions and "helping people understand more about it [OneCoin]."
He said OneCoin had not been allowed to hold presentations since the Central Bank announced its ban on the cryptocurrency.