Lets have some idea about tables should be there to implement a proper Student Attendance system in place. I have copied create script for some of my tables that used for maintaining Students record per course. I hope following sample Table scripts with relation will help you understanding regarding table structure and also to solve your issue.
Please be noted, That this table structures for your your reference only. You can add/remove tables/columns as per your requirement once you get an overall idea from this post.
CREATE TABLE `staff` (
`id` int(11) NOT NULL,
`type` varchar(200) DEFAULT NULL,
`first_name` varchar(200) DEFAULT NULL,
`last_name` varchar(200) DEFAULT NULL,
`emal` varchar(200) DEFAULT NULL,
`contact` varchar(200) DEFAULT NULL,
PRIMARY KEY (`id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
CREATE TABLE `batch` (
`id` int(11) NOT NULL,
`department` varchar(200) DEFAULT NULL,
`details` varchar(200) DEFAULT NULL,
`staff_id` int(11) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `batch_staff_idx` (`staff_id`),
CONSTRAINT `batch_staff` FOREIGN KEY (`staff_id`) REFERENCES `staff` (`id`) ON DELETE NO ACTION ON UPDATE NO ACTION
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
CREATE TABLE `student` (
`id` int(11) NOT NULL,
`batch_id` int(11) DEFAULT NULL,
`first_name` varchar(200) DEFAULT NULL,
`last_name` varchar(200) DEFAULT NULL,
`email` varchar(200) DEFAULT NULL,
`contact` varchar(200) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `batch_student_idx` (`batch_id`),
CONSTRAINT `batch_student` FOREIGN KEY (`batch_id`) REFERENCES `batch` (`batch_id`) ON DELETE NO ACTION ON UPDATE NO ACTION
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
CREATE TABLE `course` (
`id` int(11) NOT NULL,
`name` varchar(200) DEFAULT NULL,
`details` varchar(200) DEFAULT NULL,
`staff_id` int(11) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `course_staff_idx` (`staff_id`),
CONSTRAINT `course_staff` FOREIGN KEY (`staff_id`) REFERENCES `staff` (`id`) ON DELETE NO ACTION ON UPDATE NO ACTION
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
CREATE TABLE `attendence` (
`course_id` int(11) NOT NULL,
`student_id` int(11) DEFAULT NULL,
`class_date` date DEFAULT NULL,
KEY `att_course_idx` (`course_id`),
KEY `att_student_idx` (`student_id`),
CONSTRAINT `att_course` FOREIGN KEY (`course_id`) REFERENCES `course` (`id`) ON DELETE NO ACTION ON UPDATE NO ACTION,
CONSTRAINT `att_student` FOREIGN KEY (`student_id`) REFERENCES `student` (`id`) ON DELETE NO ACTION ON UPDATE NO ACTION
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
Your required data will finally store into table Attendance. From this table data, you will be able to find list of students absent/present per date and per course. Remember, the attendance table should enrich daily from a automated OR a manual process.