The accused, accountants Yobesh Amoro and David Musau Mbithi, worked in the east Africa office of the charity, formerly known as the Intermediate Technology Development Group.
The charity said that a forensic audit by PriceWaterhouseCoopers revealed it had been the victim of a "sophisticated fraud" estimated to have cost it £1.5m, between 2000 and 2003.
The fraud was reported to the Charity Commission, which decided that no inquiry was needed. The charity said all its programmes of work were still delivered.
A spokeswoman for Practical Action said: "Since the fraud, we have worked to strengthen financial management and supported the prosecution of the fraud in the courts in Kenya."
A judgement in the case is expected in September.
WorldPay has reported an increase in the number of charities noticing fraudulent activity on their accounts. The company said a common ruse used by conmen is to make small online donations to check if stolen credit cards are still active.