We know a bit about the design process that went into the Malayan flag (the ancestor of the current Malaysian flag) in 1949-50, and that can give us some insight into what was and wasn't taken from the American flag.

For example, the colour scheme of the Malayan flag is very simlar to that of the American flag, but it was arrived at independently. Red, white, blue and yellow were the most common colours on the individual Malayan state flags, so it was recommended that proposals limit themselves to those colours. Red, white, and blue were also British colours, and yellow the traditional colour of monarchy in Southeast Asia.

The pattern of the flag that was eventually chosen though very clearly shows some American influence. Those colours could have been arranged in any way, but in the end they were put into a field of red and white stripes with a blue canton. Now, the American flag wasn't the first in history that looked like this -- see for example the flags used by the East India Company -- but by 1950 it was far and away the most influential and recognizable. One specifically American innovation was to use the elements of this pattern for counting. So just like the American flag had thirteen stripes for the original thirteen states, the Malayan flag had eleven stripes and an eleven-pointed star for the eleven states in its federation.

So yes, while there were some local design elements that went into the mix, I think it's fair to say that the Malaysian flag was based on the American one.