Kovanda, who was also arrested, said he believed at the time the operation to follow the Prime Minister's wife was in the interests of national security.
But his orders came from Nagyova rather than his superiors in the Defence Ministry.
Portrayed as a femme fatale with men seemingly too eager to please her, Nagyova, 48, had apparently managed to build a mini fiefdom around her position at the heart of Necas' staff, with her power and influence extending far beyond the walls of her office.
She reportedly controlled access to the Prime Minister, also 48, and anybody who wanted to speak to him had to speak to her first.
Police accuse Nagyova of asking military spies to tail Necas' estranged wife. It is thought she cajoled friends in Czech military intelligence to find incriminating information on Radka Necasova.
Eduard Bruna, Nagyova's lawyer, has denied this, saying his client was worried that the Prime Minister's wife had fallen under the influence of Jehovah's Witnesses.
"Necasova was collaborating with people from the Jehovah's Witnesses, and had begun to collect money for presents for some people," said Bruna.
"My client thought this merited an investigation and surveillance."
Last week, Necas announced that his 25-year-old marriage was over.
Although Necas is not under investigation, and appeared to be unaware that his wife was being watched, he decided his positions of both Prime Minister and leader of the Civic Democratic Party were untenable.
"I am fully aware of the problems of my personal life burdening the political scene and the Civic Democrats at present," said Necas. "I will step down as prime minister. I am aware of my political responsibility."
The departure of Necas, who had led the Czech Republic's centre-right coalition government since July 2010, prompted political jockeying among the coalition's constituent parts to find a successor.
Martin Kuba, a Civic Democrat and Trade and Industry Minister, has emerged as favourite to fill Necas' shoes but he faces strong opposition from junior members of the coalition.
An EU member state of 10.5 million, the Czech Republic has been plagued by corruption since emerging as an independent state following its split with Slovakia in 1993.
Last year, Transparency International, a corruption watchdog, ranked it as worse than Rwanda in terms of graft prevalence.Telegraph Group Ltd