The Zoological Society of London (ZSL) says it is not clear whether the wound on the animal was inflicted before or after it died.
The young female, which was found dead on Tuesday, was first spotted around Woolwich and Dagenham, east London, over the weekend.
Its presence there was confirmed on Sunday by the British Divers Marine Life Rescue (BDMLR), which looks after the rescue and well-being of marine animals in distress around the UK.
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The BDMLR said it found the dead whale just after 5pm on Tuesday in the Greenhithe area, around 15 miles to the east.
Rob Deaville, a project manager with ZSL’s UK Cetacean Strandings Investigation Programme (CSIP), confirmed it was a juvenile female which “has a large wound indicative of a ship strike, but it is currently unknown whether this was inflicted before or after the whale’s death”.
His team will be carrying out a post-mortem on Wednesday evening, he said, hoping to learn “more about the reasons for the whale’s death and why it entered the Thames”.
The whale was first seen by long-time sailor Richard Banner, who tweeted earlier that he felt “privileged to have seen it, just wish it had been in the waters it belonged”.
Initially it seemed at home, according to Julia Cable, national co-ordinator for the BDMLR, who said it was behaving normally, but had probably made a navigational error.
Humpback whales are rarely stranded around the UK coast, with just one or two recorded on average each year.
However, this is the fifth humpback to be recorded stranded in the UK so far this year.
Two other humpback whales which have previously been recorded in the Thames and wider Thames estuary region, in 2009 and 2013 – both died.
Those that have previously made their way into the Thames have endured mixed fortunes.
In 2009, a humpback whale was found washed up on the shore in Kent, seemingly after dying from starvation.
Last year, a beluga whale, nicknamed Benny, was spotted swimming in the Thames near Gravesend but is thought to have made his own way back to sea in the new year.