Background: Patient safety involves identifying, assessing, and managing patient-related risks and occurrences to improve patient care and reduce patient harm. In Nigeria, there is a lack of studies on patient safety culture, especially in the northern part of the country. This study aimed to determine the levels and factors that contribute to nurses’ negative perceptions of patient safety culture in public health facilities. Methodology: A total of 460 nurses were surveyed across 21 secondary health facilities using the Hospital Survey on Patient Safety Culture, and the response rate was 93.5%. Descriptive statistics and multiple logistic regression were used to analyze the data. Results: The results showed that 59.8% of the respondents were female, and 42.6% were within the age range of 30–39 years old. Most of them (48.3%) had spent 1–5 years working in the hospital. Three out of 12 composite measures had higher negative responses (staffing—30.5%, non-punitive response to error—42.8%, and frequency of events reported—43.1%). A multiple logistic regression analysis affirmed that all three variables, in addition to organizational learning, were significant associated with overall negative perceptions of patient safety culture, with 3.15, 1.84, 2.26, and 2.39 odds ratios, respectively. Conclusion: The results revealed that four critical areas of patient safety required improvement; therefore, intervention is recommended to minimize unnecessary patient harm and medical expenses.