Uganda's Commissioner for Refugees Apollo Kazungu and three of his senior staff are being investigated.
Investigations will also consider whether officials from UN aid agencies were involved.
Uganda is said to host some 1.4 million refugees - welcoming more than any other country in 2016 - mostly from South Sudan and DR Congo.
But these allegations will cast doubts on those figures.
Until recently, Uganda had been widely praised for its immigration policies and described as one of the best places in the world to be a refugee.
The Ugandan Daily Monitor, which first reported the allegations, says the issue was first raised by UN country representative Rosa Malango.
The newspaper says she raised three issues, including "doubtful" numbers of refugees, the trafficking of women and children, and fraud.
One spot check in the capital Kampala found just 7,000 people when there were reported to be 26,000 needing aid, the Daily Monitor reports, leading to questions about where the money and resources for the missing 19,000 were going.
As a result of the accusations, the United States, European Union and UK are all threatening to withhold funding to the country, the UK's Guardian newspaper says.
"At the moment these are allegations and will be treated as such," a spokesman for Uganda's prime minister told the BBC.
"The investigations will determine what the facts are and what action to take. These reports do not change or deter Uganda's long-held record and commitment to providing safety to refugees."
Musa Ecweru, state minister for relief and disaster preparedness, assured the Guardian that measures would be taken to prevent any fraud in future, suggesting biometric registration for all refugees entering the country.
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