The last influenza pandemic in 2009 emerged from swine and surveillance of swine influenza is important for pandemic preparedness. Movement of swine during husbandry, trade or marketing for slaughter provide opportunities for transfer and genetic reassortment of swine influenza viruses. Over 90% of the swine slaughtered at the central swine abattoir in Hong Kong are imported from farms located in multiple provinces in mainland China. There is opportunity for virus cross-infection during this transport and slaughter process. Of the 26,980 swabs collected in the slaughterhouse in Hong Kong from 5th January 2012 to 15th December 2016, we analyzed sequence data on influenza A (H3N2) virus isolates (n = 174) in conjunction with date of sampling and originating farm. Molecular epidemiology provided evidence of virus cross-infection between swine originating from different farms during transport. The findings are also suggestive of a virus lineage persisting in a swine farm for over 2 years, although the lack of information on management practices at farm-level means that alternative explanations cannot be excluded We used virus serology and isolation data from 4,226 pairs of linked serum and swabs collected from the same pig at slaughter from swine originating from Guangdong Province to compare the force of infection (FOI) during transport and within farms. The mean weekly FOI during transport was λt = 0.0286 (95% CI = 0.0211-0.0391) while the weekly FOI in farms was λf = 0.0089 (95% CI = 0.0084-0.0095), assuming a possible exposure duration in farm of 28 weeks, suggesting increased force of infection during the transport process. Pigs sourced from farms with high seroprevalence were found to be a significant risk factor (adjusted OR = 2.24, p-value = 0.015) for infection of imported pigs during transport by multivariable logistic regression analysis, whereas pigs with HAI titer of ≥1:40 were associated with a substantial reduction in infection risk by 67% (p-value = 0.012). Transport may increase virus cross-infection rates and provide opportunities for virus reassortment potentially increasing zoonotic risk to those involved in the transportation and slaughtering processes.