Short answer in Jain Dharma

• If a woman realizes she got her periods during pooja and she truly did not know, there is no pap (fault) for the unknowing act. Intention matters in Jainism.

What to do immediately (simple maryada) 1) Stop the external ritual gently. Do not touch the murti, snatra/abhishek vessels, aarti/deepak, shastras, or the altar further. 2) Offer mental bhakti from where you are: recite Navkar Mantra softly and do a brief alochana–pratikraman in thought for any faults done unknowingly. 3) If temple/home-altar objects were touched, let another eligible person rinse and purify the items and cloths. If you are alone at home, leave them as is; clean and launder after the period ends. 4) Change clothes and maintain normal cleanliness. For the remaining days, do only manas-puja (mental worship), svadhyaya (study without touching scriptures physically), and japa at home.

After the period ends

• Bathe, wear fresh clean clothes, and then resume regular murtipuja/derasar darshan and handling of pooja items as usual.
• If you wish, do a short pratikraman or kshamapana to firm up the resolve to observe maryada ahead.

Sect-wise note

• Shvetāmbara and Digambara traditions both advise refraining from entering the garbhagriha, doing abhishek/aarti, and touching murtis or scriptures during menstruation. Mental bhakti and quiet svadhyaya are allowed. Local family or sangh practices may differ in small details; follow your guru/sangh maryada.

Essence

• Menstruation is a natural bodily process. Jain Dharma emphasizes inner purity, non-violence, and carefulness. If something happened unknowingly, do alochana–pratikraman and keep the mind peaceful; there is no need for guilt.

Helpful simple guides:

• Pratikraman (meaning and steps)
• What is followed in periods in Jainism (simple overview)
• How to perform Pratikraman (step-by-step)