The 23-year-old, who represented Ukraine at the 2020 Tokyo Olympics and the Paris Games last year, revealed the switch in an interview with a Russian newspaper earlier this week.
The federation said Lyskun had not informed them, her coaching staff or Ukraine's sports ministry about her decision.
"Such steps are categorically unacceptable," it said in a statement.
"They discredit not only an individual athlete, but also the entire team of Ukraine which every day selflessly fights for the right to represent our country in the international arena.
"The Diving Federation of Ukraine will also appeal to international sports institutions with a requirement to apply sports quarantine to this athlete in accordance with current international standards," it added.
Russian and Belarusian athletes were banned from World Aquatics events after Moscow's 2022 invasion of Ukraine, but some of their athletes competed as neutrals in the Paris Olympics as the restrictions were eased.
There was no response from the Russia's federation to a Reuters request for comment outside normal business hours.
Lyskun told Russian outlet Izvestia that she made the decision to switch allegiance after realising she was no longer growing under her coaches in Ukraine and that they were "all gymnasts or trampoline athletes".
Lyskun won 10m synchro gold for Ukraine with Kseniia Bailo at last year's European aquatics championships in Belgrade as well as team gold at the 2018 event in Glasgow.
