Piper Jaffray analyst Gene Munster estimates that 53-percent of Apple’s total addressable market for the iPhone 3G will be pre-paid customers.

The analyst believes that these customers will likely wind up paying in excess of $600 for the iPhone 3G. The estimate assumes Apple charges carriers an average $425 for the new phone and those carriers then turn around and mark up the pre-paid handsets another $175 to turn a profit.

Munster also explains in his note to clients that he expects Apple to sell 12.9 million iPhones in 2008 and 45 million in 2009, giving Apple almost 20-percent of the global mobile phone market by the end of next year.

Relating to his previous comments Munster believes that 2.7 million iPhones will be sold to pre-paid customers in 2008 and 5.7 million in 2009.

“While 17 percent may seem aggressive, Apple currently has 20 percent in North American driven by a $400 priced phone,” he told clients. “We only expect Apple to have 20 percent or greater smartphone share in two regions, North America and EMEA (Europe, the Middle East and Africa)”.

Munster retains a buy rating on Apple stock with a price target of $250.