Short answer: Yes—if it’s an urgent natural need, you may go. Do not suppress the urge.

How to do it properly (simple steps):

• Ideal is to complete Pratikraman without any break. But natural urges (vega) should not be suppressed, as that disturbs the mind and harms the body.
• Before getting up, mentally seek pardon and resolve to return and continue Pratikraman with the same focus.
• Rise calmly, keep silence, watch your steps to avoid himsa.
• After using the washroom, cleanse well; wash hands, feet, and rinse the mouth.
• Return, sit again, center the mind with Namokar Mantra, and continue from where you paused.

Sect note:

• Shwetambar: After returning, it is good practice to re‑enter the state of samayik with a brief inner pratyakhyan (intent to resume) and then proceed.
• Digambar: Sit again in the meditative posture, recite Namokar, reaffirm the samayik bhav, and continue.

If the break will be long (e.g., for bowel movement), it is better to conclude respectfully and later do Pratikraman again with full attention.

Practical tip: Use the washroom just before starting Pratikraman and avoid excess food/water right before, so you can maintain uninterrupted focus.