If the contractual probation period is longer than the 3 months minimum qualifying period, will the employee enjoy maternity protection?

Yes.

The maternity protection will apply to the employee as long as she has served her employer for at least 3 continuous months.

The probationary status will not affect employee's right to maternity protection. The 3 months qualifying period is generally considered a reasonable period of time for an employer to assess a female employee's suitability for employment.