The BBC Sports presenter made a sarcastic comment in response to a tweet by the Good Morning Britain host highlighting the death of migrant workers while building the new stadium for the football tournament in Doha.
Lineker replied: "Tragic. If only we’d covered the migrant deaths and worker’s rights abuses…"
Rinder retorted: "I’m aware of the excellent work of BBC journalists. No doubt your punditry has taken equal courage. I just wonder if you think it was wise judgment or a good use of your considerable platform to celebrate your ‘favourite stadium’ given the migrant deaths you (‘we’) have covered."
The Match Of The Day host had shared a picture of the stadium lit up at night captioned "Might be my favourite stadium."
Rinder responded with a photograph of a migrant worker who died captioned: "Mohammad Shahid Miah, 29, from Bangladesh, died when floodwater in his room came into contact with an exposed electric cable, electrocuting him. One of the countless human beings building your favourite stadium @GaryLineker."
Lineker has come under fire, along with other sports presenters including Alex Scott and Gary Neville for accepting paid work covering the World Cup in Qatar, in spite of the host country's human rights abuses of gay people, women and migrant workers.
The 61-year-old former England player pledged ahead of the tournament to address the issues as part of the BBC coverage of the World Cup.
He said: "We’ll be addressing the issues, we’ll be talking about them. And that’s the whole thing that we’re going through at the moment, is how do we do that.
“We’ve got the opening game and I’m sure we’ll discuss the issues of human rights, homophobia, of the problems with the stadiums and the lives of lost and workers’ rights, etc.”
Homosexuality is illegal in Qatar and Muslims can face the death penalty if prosecuted for it.
Rinder has previously criticised David Beckham for accepting a £10milion position as an ambassador for the World Cup before it began in Qatar.
He told the Mail On Sunday: “There should be basic requirements before you are entitled to [host] them, and that’s not just about LGBTQ.
“It’s about the 6,500 workers who died, it’s about the fact that Beckham’s daughter Harper would not be able to continue with her education [if she was Qatari] without the permission of a male relative."
Rinder is a qualified lawyer, who rose to fame as the star of reality courtroom show Judge Rinder in 2014. He competed in Strictly Come Dancing in 2016 and now presents GMB as part of a rosta of rotating co-hosts since Piers Morgan quit the show.
Watch: Richard Madeley accuses Gary Lineker of hypocrisy over Qatar criticism