But it has dismissed as fake a widely circulated statement that purports to show that using the airline would have been cheaper for the president.
Despite his explanation, many Kenyans have criticized the president.
Mr Manyora says the president should have explained himself better, to persuade people that it was right to use a private jet.
He said the president should have “considered people’s perceptions” and explained the benefits of using a chartered plane, including flexibility, class and security.
“I would have expected that kind of explanation, not one that leaves people wondering,” he said.
On social media some criticised the president for using an airline owned by another country.
“It is a shame as a country if the president can’t use our national airline, Kenya Airways because it is expensive,” said Alinur Mohamed.
Calculating the total cost of business class tickets for the president and his delegation, local media report this would have been far cheaper than hiring a jet.
The president used a Dubai-owned RoyalJet company to travel to the US, along with an entourage of about 30 people.
Hiring such a jet is reported to cost $1.5m (£1.2m) versus the $300,000 estimated cost for business-class tickets on Kenya Airways for the entire delegation.
But Mr. Ruto told US broadcaster Voice Of America (VOA) over the weekend that the estimated cost of his trip was “completely exaggerated”.
He did not respond to a direct question about how much it cost, but said the amounts being “bandied around are ridiculous”.
“I’m careful about the resources that I spend,” he added.
Last week, government spokesman Isaac Mwaura told the BBC that the “benefits from this visit far outweigh” the costs, without confirming the sums involved.
The row comes amid concerns by critics that taxpayers’ money has been used to fund extravagance in government while taxes have been raised on the basis that the state needs extra funding.
Mr Ruto has made more than 50 visits abroad since he became president in 2022 – averaging more than three a month.
The government has defended the trips as necessary – while pointing to recent directives to cut spending.