Šakalienė insists she was fired because she fell ill with cancer, whereas the founders of the non-governmental human rights organization say the decision has been long in consideration and was made due to poor management.
Šakalienė, who has been working in Human Rights Monitoring Institute (HRMI) since 2004 and was heading it for the last two years, broke the news of her dismissal on her Facebook page last Friday.
She said she was fired after refusing to sign a letter of resignation, which would have meant foregoing severance pay.
Šakalienė was diagnosed with thyroid cancer last summer. She suggested that the disease, which had forced her to take several extended periods of sick leave, was the primary reason she was being dismissed.
However, following Šakalienė's public statements about her dismissal, three co-owners of HRMI responded that they had been monitoring the institute's operations and finance for quite some time. They said the decision to relieve Šakalienė of her duties was made as a response to "serious management and financial administration issues" that had been identified.
"We value Ms Šakalienė as a competent human rights expert and resolute defender of human rights who defends the principles of liberal democracy with devotion, efficiently communicates well-reasoned comments and proposals, based on HRMI studies and her own expertise, to Lithuanian and Lithuanian institutions as well as society at large," HRMI co-owners Henrikas Mickevičius, Arūnas Pemkus and Dainius Pūras said in the statement.
"Unfortunately, having analysed processes in HRMI operations of the last several years, we must conclude that there have been accumulating unsolved problems in the way the organization and its finances were run; the psychological atmosphere in the office has been deteriorating and increasingly interfering with work. We concluded that the organization had been mismanaged," they said in the statement.
Meanwhile Šakalienė said she had trusted her team that managed the organization's day-to-day operations and had never heard any issues raised before.
"The co-owners have doubts about management and finance, but I have always trusted my team and do not see any reasons now not to. I've trusted employees in charge of finance. I've been making my decisions based on information they supplied and I think I was right in doing so. Especially since the institute's annual reports have been great. Both the board and the institute's owners praised me, I had no complaints," Šakalienė told LRT television on Monday.
Arūnas Pemkus, one of the co-owners of HRMI, said it was accepted practice to offer employees to sign a letter of resignation so as not to compromise their future employment prospects. He added he had been authorized to negotiate a bigger severance package with Šakalienė than the equivalent of two-months pay specified in the Labour Code.
The Human Rights Monitoring Institute (HRMI) was founded in 2003 in Lithuania as a human rights watchdog organisation. Since 2012, it has been the national administrator of the EEA Grants NGO Programme in Lithuania.