The Internal Revenue Service's efforts to combat a surge in identity theft are yielding success but also a side effect: delayed tax refunds for many legitimate filers.

The agency says it has strengthened the electronic system used to screen returns for potentially fraudulent refund claims by thieves who often use other people's Social Security numbers or other identifying information. When the computer detects reason to suspect fraud, it refers a tax return for investigation, holding up the refund for weeks.

This...