Oppure ancora:

codice:
package prova;

import java.util.Map;
import java.util.Set;
import java.util.TreeMap;

public class Esempio {

	public static void main(String[] args) {
		Object[][] A1 = { { 1, 5, 9 }, { 4, 6, 10 }, { 3, 0, 9 } };
		Object[][] A2 = { { 0, 9, 9 }, { 2, 1, 10 } };
		TreeMap<Object, Object[]> tm = new TreeMap<Object, Object[]>();
		tm.put(A1[0][0], A1[0]);
		tm.put(A1[1][0], A1[1]);
		tm.put(A1[2][0], A1[2]);
		tm.put(A2[0][0], A2[0]);
		tm.put(A2[1][0], A2[1]);
		Set<Map.Entry<Object, Object[]>> set = tm.entrySet();
		int m = set.size();
		Object[][] B = new Object[m][];
		int j = 0;
		for (Map.Entry<Object, Object[]> me : set) {
			B[j] = new Object[me.getValue().length];
			B[j] = me.getValue();
			j++;
		}
		System.out.println("Verifica: "+B[3][2]);
	}
}
Si può fare di meglio?