A spokesperson from the Ministry of Foreign Affairs and Trade confirmed that the funding had finished on August 30.
"Funding provision had been made for possible expansion to a third country in 2018/19 but a decision was made by CHAI to focus on Rwanda. As a consequence this funding was not drawn down.
"We are exploring how we may best provide support to Rwanda's agriculture sector," a spokesperson for Mfat said in a statement.
To date US$7.7 million ($10.4m) has been provided to CHAI activity since 2014.
Taxpayers' Union executive director Jordan Williams welcomed the news.
"Australia stopped payments in late 2016, but New Zealand has been keeping the lie that the money was effective for Rwanda and Ethiopian aid, even though those countries are not in New Zealand's aid priorities."
According to news.com.au, the Australian Government confirmed it would stop funding CHAI in 2016.
Williams said the Taxpayers' Union has collected nearly 7000 signatures calling for Foreign Minister Winston Peters to stop the funding.
"Finally, he has listened."
CHAI began as an initiative under the Clinton Foundation – founded by former US President Bill Clinton and former Secretary of State, and US presidential hopeful, Hillary Clinton.
But it was separated out to a non-profit organisation with a focus on reducing the cost of HIV/AIDS medicine in sub-Saharan Africa.
During the 2016 US presidential elections, Donald Trump was critical of the Clinton Foundation, accusing his Democratic rival of "pay for play".