Estonia is the second foreign country to use the system, which can detect an enemy radar system, after the United States bought the equipment last year.
"The delivery (to Estonia) will materialise in the very near future," Kuehnl said after meeting Estonian Foreign Minister Urmas Paet in Prague.
Last year the Czech Republic backed down on a controversial deal to sell the system capable of detecting stealth aircraft to China after pressure from the United States.
Czech company Omnipol had been granted a two-year export licence in January 2004 to export six units of the sophisticated equipment worth around 1.5 billion koruna to China by the ministry of industry and trade.
But the licence was revoked, several days after a press report said the United States was ready to bid on the Vera radar system in order to keep it from falling into the hands of the Chinese.
Omnipol said last month it was appealing the decision.
The Vera passive radar system, produced by Czech company Era, sends, receives and processes signals. It can detect and identify a non-allied radar without being detected itself and can monitor up to 200 planes simultaneously, accurately defining the target's distance and altitude.
Interest in Vera has also been shown by Malaysia, Vietnam and China.
According to the online version of Czech business weekly Euro on Tuesday, Chinese politicians tried to persuade Czech Prime Minister Jiri Paroubek, who has been on an official visit to China this week, to sell the radar system to China.
Chinese representatives reportedly said they would not discuss certain contracts unless there was progress in the negotiations on Vera.
The Czech delegation, however, rejected the Chinese conditions, Euro Online wrote.
Vera is a successor to a similar Czech system, Tamara, which was believed to have been used in the NATO bombing of Yugoslavia in 1999.