Is it legal if the company that I work for makes only the women punch a time clock?

If only the women were hourly workers, this would be legal: hourly workers have to punch clocks, so there'd be nothing discriminatory in making the hourly workers, who happen to be women, do this.

But that is not what you describe. You describe salaried women--i.e. workers for whom hours worked do not affect pay--having to punch a time clock, while salaried men do not. On the face of it, you have described illegal sex-based discrimination, because a company cannot treat women differently simply or only because they are women.

It is also possible that the women should be punching clocks because whether or not they are salaried, it may be that they are eligible for overtime: it is NOT the case that all salaried employers are overtime exempt, but rather, to be exempt, you need to be paid on a salary basis and also meet one or more of the tests for exemption. You can find those tests at the U.S. Dept. of Labor website, but in brief, you need to have a reasonable amount of discretion and authority, in addition to being salaried, to be overtime exempt, and many office workers do not in fact meet these tests. (Non-exempt salaried workers receive extra pay for working more than 40 hours in a week.) Of course, even if the women should track hours for overtime purposes, that doesn't explain why men with similar jobs would not--again, you can't treat women and men differently only on account of their sex.

So there may be illegal discrimination going on, and there may also be wage-and-hour (overtime) violations. The women should consult with an employment law attorney about their situation, to see what their rights and options are.