Martin, 28, has scored seven goals in 17 appearances for Fulham in the Championship this term.
He "made himself unavailable" for Friday's abandoned game at Reading, but Jokanovic insisted he would stay.
"I'm not going to send him back to Derby - he's going to stay with us and respect the contract," said Jokanovic.
"He stopped in training, but I have information from the medical staff that he is available to play. He decided to take a day off."
He continued to BBC Radio London: "We're not a train station, you can't come in and out when you want. We need to respect ourselves, we are the oldest London club.
"I don't know if he will play for Fulham, but I'm sure he's not going to play for Derby."
Earlier this month, Derby manager Steve McClaren said he was surprised Martin was allowed to leave the club under previous boss Nigel Pearson.

Jo Deering died in 2011, aged 52,  just months after being sectioned under the Mental Health Act.
Under-fire Southern Health NHS Foundation Trust admitted it could have made better decisions about her care.
However, Ms Deering's sister, Maureen Rickman, said the trust's findings "deserved to be binned".
In December, the BBC revealed that the trust, which provides services to about 45,000 people in Hampshire, Dorset, Wiltshire, Oxfordshire and Buckinghamshire, had failed to investigate hundreds of unexpected deaths since 2011.
Ms Deering, from New Milton, Hampshire, had paranoid schizophrenia and was discharged from hospital two weeks after being sectioned.
She was sent home where she was the main carer for her 89-year-old mother, who had dementia. Four months later she took her own life.
Her family said the trust should not have allowed her to go home while she was still ill.
In its 2012 report, the trust said the medical team based at Waterford House who cared for Ms Deering should "be commended for their ongoing efforts to work with Joanna and her whole family in as an inclusive a way as possible, despite significant complications".
Ms Rickman said: "There isn't an investigation here, nothing of the sort. I could have carried out a better investigation myself to be quite frank."
She added: "It deserves to be binned - nobody would have known anything from this at all, there is nothing to take away from this other than a load of psycho babble and twaddle."
In a statement, Dr Lesley Stevens, medical director at the trust, said the report found its "decision-making process about granting leave, and how we communicated this with Jo and her family, could have been better".
"Robust actions to learn from this incident were fully implemented at the time," she added.
She said the trust had provided community support to help Ms Deering with her role as a carer.
"The way we investigate and learn when things go wrong, has changed substantially," she added.

The CM11 armoured vehicle carrying five soldiers was returning to base when it fell into the Wangsha river in Pingtung county in the south of the country.
The driver and tank captain survived.
The drill was part of preparations for next week's annual Han Kuang military exercise. President Tsai Ing-wen has sent her condolences.
The CM11 was returning from a firing test at about 10:30 local time (02:30 GMT) when an apparent mechanical failure in one of the tracks left the driver unable to make a required left turn, the army said.
The driver was able to escape with light injuries.
The four others were pulled unresponsive from the vehicle. The captain was revived and later taken to a military hospital in neighbouring Kaohsiung city.
The soldiers reportedly belonged to the Eighth Army Command.
President Tsai demanded a speedy investigation into the cause of the incident.
She is scheduled to preside over the military exercises, which simulate possible attacks by Beijing.
Fulham manager Slavisa Jokanovic has dismissed reports that striker Chris Martin could return early to Derby from his season-long loan at Craven Cottage.
[NEXT_CONCEPT]
The family of a woman who killed herself after being discharged from hospital has labelled a report into her death "psycho babble and twaddle".
[NEXT_CONCEPT]
A Taiwanese armoured vehicle has plunged from a three-metre bridge in heavy rain after a military drill, killing three soldiers, officials say.