When money is entered in the system, it becomes electronic. The money is stolen the same way hackers steal from banks. With insider help so much is possible.

Kenya has seen nothing yet on cyber crimes

so what you are saying is that KRA has electronic money in its systems?

PALO ALTO, Calif. — In late 2013, an A.T.M. in Kiev started dispensing cash at seemingly random times of day. No one had put in a card or touched a button. Cameras showed that the piles of money had been swept up by customers who appeared lucky to be there at the right moment.

But when a Russian cybersecurity firm, Kaspersky Lab, was called to Ukraine to investigate, it discovered that the errant machine was the least of the bank’s problems.

The bank’s internal computers, used by employees who process daily transfers and conduct bookkeeping, had been penetrated by malware that allowed cybercriminals to record their every move. The malicious software lurked for months, sending back video feeds and images that told a criminal group — including Russians, Chinese and Europeans — how the bank conducted its daily routines, according to the investigators.

Then the group impersonated bank officers, not only turning on various cash machines, but also transferring millions of dollars from banks in Russia, Japan, Switzerland, the United States and the Netherlands into dummy accounts set up in other countries.

the only way this whole thing makes sense is if a guy reduced tax obligations of certain companies and the sum total reduction was 4B and was paid by the said companies a fraction of the amount he "saved" them from.
Nothing else makes any sense!! nothing!! Kuiba from Kra? thats like stealing from their bank accounts... thats on the banks side. not KRA!! nothing about the 'stealing from KRA' claim makes any sense!

Back to the article.

had been robbing banks using Salami attacks and electronic transfers

They have also been colluding with motor vehicle importers to evade tax and were illegally registering them.

What about payments? What's the system for payments like especially via EFT?

Some organizations implement solutions that will generate a file which when sent to the bank executes a payment