Here's how Danny Kaye sang it on "Tubby the Tuba and Other Favorites":

There's a hole...a log...a branch...a bump...a frog...a tail...a fly...a speck...a fleck.

On the last verse (fleck), he sings the first line and then the chorus (which has been singing the second line each time) says, "There's a WHAT?" and he replies, "Like I said--in the bottom of the sea."

Then after the last verse he sings, "So let's...
flick the fleck
brush the speck
swat the fly
twist the tail
chase the frog
flatten the bump
break the branch
burn the log
fill the hole,
Hole in the bottom of the sea
'Cause we need it like a hole...in the sea...in the sea...in the sea"

Aloha,
Mark

(that's from memory...and I'll stand on its accuracy!)