The claim came after a court on Monday overturned a five-month suspension handed to Veronica Abad by the labor ministry due to alleged neglect of duties related to her role as a Middle East peace envoy.
Following the ruling, Noboa's government assigned Abad the sole function of promoting Ecuador's economic relations with Turkey, telling her to report for duty there by December 27.
The appointment "is a new insult to Ecuadorians, seeking my immediate banishment to 'Turkey,'" Abad wrote in a letter published on social media.
Abad and Noboa have a fraught working relationship, despite pairing up on a successful ticket in 2023 elections.
He has dropped her as his vice president pick in elections to take place on February 9. And on Monday he said in a radio interview it had been a "mistake" to make her his election partner.
Under Ecuador's constitution, Noboa is permitted to campaign for re-election on condition that he hands over his powers to his vice president during that period.
Noboa named Abad peace envoy to Israel in December 2023, effectively removing her from Quito and day-to-day government business.
A rise in tensions in the Middle East late this year prompted the government to tell Abad to relocate to Turkey for her security.
The labor ministry said that she was meant to have gone to Ankara on September 1 but that she arrived five days later.
It argued that constituted an abandonment of her envoy role and it ordered the five-month suspension of her position as vice president.
Judge Nubia Vera said on Monday that Abad's constitutional rights had been trampled.
She ordered the labor ministry to issue an apology and pay Abad's lost salary.
Vera told reporters she had been "coerced, threatened, intimidated" by judicial branch officials to rule against Abad, but had refused, putting her career "at stake."
After the ruling, Abad said that she was prevented by the military from entering the office of the vice president, and filed a complaint with the public prosecutor's office.
