The 34-year-old TV presenter is in South Africa for some episodes of the ITV2 show, but hosts the series spin-off AfterSun from the UK.
She also hosts a Sunday morning BBC Radio 5 Live show from the UK.
After a fan questioned why she did not broadcast her radio show and AfterSun from Cape Town, Whitmore responded and said she only travelled to to South Africa for some parts of Love Island.
She added she was an advocate of offsetting her carbon footprint.
Twitter user, Jane Clapton, wrote online: "@bbc5live why is Laura Whitmore flying from South Africa every weekend to do her Sunday morning radio show then back to SA to present Love Island? Surely there are studios she could broadcast from in SA? #ClimateCrisis."
However, Whitmore replied: "Hi Jane, love island aftersun is filmed in London - as all the guests are based in the UK.
"I'm only in cape town for the finale, public voting etc."
"And I'm an advocate of offsetting carbon footprint you'll notice on my Twitter," she added.
Another user wrote: "I’m sorry but you could easily do your radio live in South Africa and easily present love island aftersun (I’m sure itv2 could pay for guests to fly out)!
"I think it’s ridiculous that you’re travelling back and forth! You need to think more of the climate! #ClimateCrisis."
But there were other people who supported the presenter's choices, with one posting: "It’s quite ridiculous to expect guests from both Laura’s radio show and aftersun to fly over ten hours.
"Plus they still have to get back somehow and that would cause more of a carbon footprint. Think before you accuse people of things."
Just days before the Twitter spat, Whitmore tweeted about offsetting your carbon footprint.
She wrote: "There's some amazing projects out there that you can use to offset your carbon footprint.
"Check them out!"