Background. A timely detection of outbreaks through surveillance is needed in order to prevent future pandemics. However, current surveillance systems may not be prepared to accomplish this goal, especially in resource limited settings. As data quality and timeliness are attributes that improve outbreak detection capacity, we assessed the effect of two interventions on such attributes in Alerta, an electronic disease surveillance system in the Peruvian Navy. Methods. 40 Alerta reporting units (18 clinics and 22 ships) were included in a 12-week prospective evaluation project. After a short refresher course on the notification process, units were randomly assigned to either a phone, visit or control group. Phone group sites were called three hours before the biweekly reporting deadline if they had not sent their report. Visit group sites received supervision visits on weeks 4 & 8, but no phone calls. The control group sites were not contacted by phone or visited. Timeliness and data quality were assessed by calculating the percentage of reports sent on time and percentage of errors per total number of reports, respectively. Results. Timeliness improved in the phone group from 64.6% to 84% in clinics (+19.4 [95% CI, +10.3 to +28.6]; p < 0.001) and from 46.9% to 77.3% on ships (+30.4 [95% CI, +16.9 to +43.8]; p < 0.001). Visit and control groups did not show significant changes in timeliness. Error rates decreased in the visit group from 7.1% to 2% in clinics (-5.1 [95% CI, -8.7 to -1.4]; p = 0.007), but only from 7.3% to 6.7% on ships (-0.6 [95% CI, -2.4 to +1.1]; p = 0.445). Phone and control groups did not show significant improvement in data quality. Conclusion. Regular phone reminders significantly improved timeliness of reports in clinics and ships, whereas supervision visits led to improved data quality only among clinics. Further investigations are needed to establish the cost-effectiveness and optimal use of each of these strategies.