The agency said "opportunists or touts" had tried to take advantage of its offer for those who were at the Ariana Grande concert at Manchester Arena.
It has said fans at the original show can get into Sunday's event for free.
Some 25,000 people applied - but just 14,200 were at the concert on 22 May.
Twenty-two people died and 116 were injured in a suicide bombing at the end of Grande's show.
Sunday's concert - One Love Manchester - is expected to raise £2m for the victims and their families.
Grande will be joined by stars including Robbie Williams, Little Mix, Take That, Katy Perry, Miley Cyrus and Justin Bieber.
The deadline for fans who were at the original concert to apply for free tickets for Sunday was extended twice, eventually closing at 14:00 BST on Thursday.
In a statement, Ticketmaster said: "We have set aside tickets for the 14,200 people who were at the Ariana Grande concert to attend One Love Manchester for free.
"More than 25,000 people applied for them. Sadly, over 10,000 unscrupulous applications have been made.
"At Ticketmaster we are doing everything we can - including extending today's deadline - to ensure that tickets go to the actual fans and not the opportunists or touts who have also been applying for free tickets."
As well as offering free tickets to those at the original concert, the company put around 35,000 further tickets on general sale on Thursday for £40 each. They sold out in less than 20 minutes.
But some have appeared on eBay for up to £200 each, leading fans on social media to vent their anger at the "absolutely sickening" sellers who were trying to cash in.
The auction site said it was removing them as fast as it could.
EBay said it doesn't normally allow the sale of any type of ticket, so any listings for Sunday "will be removed automatically". But some did slip through the net.
The eBay statement continued: "All tickets for this event will most certainly be removed by the team who are doing manual sweeps to pick up any that slip through.
"We also aren't allowing the sale of any item which profits in any way from the tragedy in Manchester. All of these items are being removed if they appear, and the sellers' accounts will be restricted."
And Ticketmaster said: "We are cancelling tickets of those who are reselling wherever possible."
Meanwhile, the four main online ticket marketplaces - Get Me In!, Seatwave, Viagogo and Stubhub - said they would not list any tickets for the show.
No tickets were listed on those sites at the time of writing.
The three-hour event will be staged at Old Trafford cricket ground and will be broadcast live on BBC One in the UK.