The most common and most likely answer to this crossword clue is the 6 plus 7 letter word PARENT COMPANY
I've seen this crossword clue in The Daily Telegraph
P
A
R
E
N
T
C
O
M
P
A
N
Y
More clues leading to the result PARENT COMPANY
Buddy explains!

The straight part
We know that "controlling organisation" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case controlling organisation = parent company.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.