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The antiviral efficacy of cell-extracts (CEs) derived from cypress (<i>Chamaecyparis obtusa</i> (Siebold & Zucc.) Endl., <i>C. obtusa</i>) and cedar (<i>Cryptomeria japonica</i> (Thunb. ex. L.) D.Don, <i>C. japonica</i>) was assessed using phi6 and MS2 bacteriophages, which are widely accepted surrogate models for enveloped and non-enveloped viruses, in order to verify their potential use as antiviral agents. Our results indicate that CEs derived from <i>C. obtusa</i> are dominantly composed of terpinen-4-ol (18.0%), α-terpinyl acetate (10.1%), bornyl acetate (9.7%), limonene (7.1%), and γ-terpinene (6.7%), while CEs derived from <i>C. japonica</i> are dominantly composed of terpinen-4-ol (48.0%) and α-pinene (15.9%), which exhibited robust antiviral activity against phi6 bacteriophage. Both CEs successfully inactivated the phi6 bacteriophage below the detection limit (10 PFU/mL) within a short exposure time of 30 s (log reduction value, LRV > 4). Through exposure experiments utilizing CEs with content ratios prepared via 2-fold serial dilutions (ranging from 3.13% to 100%), we demonstrated that the antiviral effect could be sustained up to a concentration of 25% (<i>C. obtusa</i> LRV = 3.8, <i>C. japonica</i> LRV > 4.3 at a 25% CE content ratio for each species). However, CEs with content ratios below 12.5% did not produce a significant reduction in bacteriophage concentration and consequently lost their antiviral effects. Conversely, both CEs did not exhibit antiviral activity against MS2 bacteriophage, a non-enveloped virus. Our findings reveal for the first time the potential of CEs derived from <i>C. obtusa</i> and <i>C. japonica</i> for use as antiviral agents specifically targeting enveloped viruses.