The Care Minister appeared on Wednesday's show (April 22) for the second time to discuss the government's latest developments in fighting coronavirus.
However, those complaints have now rose to 1,910, the TV watchdog has confirmed.
During today's interview, Piers accused Ms Whately of "waffling" rather than giving straight answers.
At what point will you come back and have an answer?
The presenter brought up Ms Whately's interview last week in which she "didn't know" how many people had died in care homes.
He said: "At what point will you come back and have an answer?
"This is your job to know this stuff. These are elderly vulnerable people dying of COVID-19 and you are not taking their deaths seriously enough."
Ms Whately hit back: "That's an incredibly unreasonable accusation. I take every single death extremely seriously..." as Piers started interrupting her.
She asked: "Can I finish my sentence? The problem is you just keep on interrupting me and I can't explain what we're doing."
Piers hit back: "You don't have any answers, you just waffle."
Some viewers accused Piers of "bullying" the care minister and he denied the claims on Twitter.
Piers slams 'bullying' claims
He wrote: "It's not 'bullying' or 'hounding' or 'unfair' to push a Care minister hard on how many care home residents & workers have died from COVID-19.
"It's called 'holding Govt to account'.
"The Govt is grossly understating the real number, I suspect for political reasons."
On today's GMB, Piers demanded to know why there has been a decrease in the number of coronavirus tests being handed out in the UK.
The target is 100,000 tests per day by the end of April however, there had only been 18,000 new tests carried out yesterday (April 21).
Piers raged: "It's now April 22nd and we're testing less people yesterday than we tested 12 days ago which I would argue, is a spectacular failure."
Ms Whately replied: "We know that testing is really important and we have been working hard to ramp up the testing capacity..."
However, Piers cut in: "I down wanna hear about you ramping up though, with respect you're not ramping it up."
Ms Whately said: "Well if you'll let me finish speaking," to which Piers interrupted: "But you're answering different questions."
Good Morning Britain airs on ITV, weekdays, at 6am.
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